Homebrew [RELEASE] Howling Theme Tool - Create your own CIA theme packages with Custom and Official themes

[Welcius]

Unless you have linked NANDS the answer is no, 'cause the payloads in themedata for ThemeHax/ShuffleHax are located on SysNAND.

Would I be able to install HomeMenuHax via BrowserHax again on emuNAND if I change my opinion?

 

[Chelsea_Fantasy]

I tried with DevMenu and it worked. Don't know why FBI didn't.

FBI haves some serious issues with multicontent unsigned cias

Does the themes interfere with HomeMenuHax? Would I have to reinstall it? Thanks in advance

EDIT: I want to use them on emuNAND

if your nands are unlinked there is no problem (the nand using themehax must be your sysnand and the one using custom themes, the emunand)

No one have an idea of how can I backup my official themes?

There is a lot of tutorials on how to backup eshop games. They also work for themes.
In small words, console-decrypt your content file and themes, then use makerom to make a CIA package. Backup done.

Here's the screenshot showing the previews and another showing what every folder has (since all where downloaded from 3dsthem.es) except the ones that don't have music don't have the music files obviously. The Checker tools lists them all as in good condition.
It doesn't affect certain themes specifically, it can be any theme that's last or first in the list.

Hey i would like to add on that i am having the same exact issue , all of folders are in the correct format and i have the themes listed in A - Z format.I had 21 Themes compiled and when i install them on the 3DS only 19 appear for me the last two themes do not appear.

Also thanks for your hard work this is an excellent tool nonetheless! but i figured we should bring this to your attention

@AkitoUF te responderé por PM
translation: I will reply you by PM
@Anim3 I will try to fix the issue. I will talk with @AkitoUF to see some details, then will reply you in this thread

--------------------- MERGED ---------------------------

Would I be able to install HomeMenuHax via BrowserHax again on emuNAND if I change my opinion?

Use the CIA hax in EmuNAND and the Theme Hax in SYSNAND

 

[UraKn0x]

FBI haves some serious issues with multicontent unsigned cias

if your nands are unlinked there is no problem (the nand using themehax must be your sysnand and the one using custom themes, the emunand)

There is a lot of tutorials on how to backup eshop games. They also work for themes.
In small words, console-decrypt your content file and themes, then use makerom to make a CIA package. Backup done.


@AkitoUF te responderé por PM
translation: I will reply you by PM
@Anim3 I will try to fix the issue. I will talk with @AkitoUF to see some details, then will reply you in this thread

--------------------- MERGED ---------------------------


Use the CIA hax in EmuNAND and the Theme Hax in SYSNAND

Is there a way to get this working on Gateway EmuNAND or do you not know?

 

[Chelsea_Fantasy]

Is there a way to get this working on Gateway EmuNAND or do you not know?

There is not way actually.
Gateway forget to patch all the signatures checks in their launcher.
True, they patched game's signature patches, but not downloadable content's patches.
If a DLC content it's fully decrypted, it will not work on Gateway.
Send an e-mail to GW asking for it.

 

[titoEarly]

I've been reading the thread and although some of you here seem to have the same issue, you haven't been given the right answer or at least one that works for me, so I would appreciate some help:

I will describe step by step what I did so you can analyze if I did something wrong:

1) Downloaded Howling Theme Tools and added 2 official themes to the list.
2) Checked them before with the check tool (everything's alright)
3) Created a .CIA with these two themes.
4) Put it on my SD Card and installed it with FBI.
5) I have them both as if I had bought them, good.

So far everything is okay. Let's call these 2 themes X and Y, now:

6) I decide to remove them from the Theme menu (I mean the one where you are allowed to choose which theme you want to use)
7) They were succesfully removed and after that I add 2 new official themes, which I'll call Z and W for future reference, in Howling Theme Tool, so now I have the 2 I used before and 2 new ones.
8) Pack 'em and put it on SD.
9) install them through FBI and
10) There's only 2 (out of 4) themes in the list, and the names are X and Y
11) When I select X it loads X but when I choose Y it loads Z.
12) uninstall them
13) Remove Y from the pack so now I only have 3: X, Z and W.
14) install the CIA, now I have 2 themes which are X and Y (Y is not supposed to even install since I removed it from the pack).
15) uninstall them by going to system preference > 3ds > downloaded content > themes > delete
16) install using FBI, and now I got X and Z but W is missing.

So, it seems I can only have 2 themes max installed? I don't know what's causing this and I've read some of you recommend Big Blue Menu instead of FBI but I haven't been able to find it and I'm not quite sure if that'd solve the problem, since they're mostly the same?

Any help will be appreciated, thanks for your time.

tl;dr
Having troubles installing more than 2 themes, only 2 themes max will appear and sometimes with names that doesn't match the theme. Sometimes even old ones that no longer are in the past end up being installed.

 

[Chelsea_Fantasy]

I've been reading the thread and although some of you here seem to have the same issue, you haven't been given the right answer or at least one that works for me, so I would appreciate some help:

I will describe step by step what I did so you can analyze if I did something wrong:

1) Downloaded Howling Theme Tools and added 2 official themes to the list.
2) Checked them before with the check tool (everything's alright)
3) Created a .CIA with these two themes.
4) Put it on my SD Card and installed it with FBI.
5) I have them both as if I had bought them, good.

So far everything is okay. Let's call these 2 themes X and Y, now:

6) I decide to remove them from the Theme menu (I mean the one where you are allowed to choose which theme you want to use)
7) They were succesfully removed and after that I add 2 new official themes, which I'll call Z and W for future reference, in Howling Theme Tool, so now I have the 2 I used before and 2 new ones.
8) Pack 'em and put it on SD.
9) install them through FBI and
10) There's only 2 (out of 4) themes in the list, and the names are X and Y
11) When I select X it loads X but when I choose Y it loads Z.
12) uninstall them
13) Remove Y from the pack so now I only have 3: X, Z and W.
14) install the CIA, now I have 2 themes which are X and Y (Y is not supposed to even install since I removed it from the pack).
15) uninstall them by going to system preference > 3ds > downloaded content > themes > delete
16) install using FBI, and now I got X and Z but W is missing.

So, it seems I can only have 2 themes max installed? I don't know what's causing this and I've read some of you recommend Big Blue Menu instead of FBI but I haven't been able to find it and I'm not quite sure if that'd solve the problem, since they're mostly the same?

Any help will be appreciated, thanks for your time.

tl;dr
Having troubles installing more than 2 themes, only 2 themes max will appear and sometimes with names that doesn't match the theme. Sometimes even old ones that no longer are in the past end up being installed.

--ENGLISH:
Error 1: NEVER use FBI to install theme packages. Use BBM (BigBlueMenu) instead.
Error 2: Delete the installed theme package before installing a new theme package.
Solution:
1-Delete the installed theme package with BBM (HMMP, HMME or HMMJ) (it's the first one down Browser for US / EU / JP)
2-Choose simple red and blue as shuffle themes to prevent garbage shuffle when the new package it's installed.
3-Install the new package.

--SPANISH:
Error 1: NUNCA uses FBI para instalar un paquete de temas. Usa BBM (BigBlueMenu) en su lugar.
Error 2: Elimina el paquete de temas que tengas instalado antes de instalar un nuevo paquete de temas.
Solución:
1-Elimina el paquete de temas instalado usando BBM (HMMP, HMME o HMMJ) (es el primero por debajo de Browser for US / EU / JP)
2-Elige rojo y azul simple como favoritos para prevenir errores haciendo shuffle una vez el nuevo paquete sea instalado.
3-Instala el nuevo paquete de temas.

 

[redunka]

There is not way actually.
Gateway forget to patch all the signatures checks in their launcher.
True, they patched game's signature patches, but not downloadable content's patches.
If a DLC content it's fully decrypted, it will not work on Gateway.
Send an e-mail to GW asking for it.

Actually, I don't think that Gateway team will ever fix this issue.
I have tried to email them about that few month ago and they just ignored it, didn't even reply.
By the way, GW has this problem not only with DLC, but also with any other non-executable
NCCH containers (CFA), such as digital manuals and Download Play. Because of that,
there is also a big problem for GW users with cryptofixing eShop games which have these partitions.

 

[SuperNintendo64]

Im getting an error... i think im the first one.

I can check the folders
I can create the CIA
I can install the CIA with several themes....

Yet on the menu i can only see ONE theme installed
It isnt the only one in its folder. It starts with A.

Tried twice. Second time i remade the CIA. Nothing.


Using FBI

 

[TUK_Pyroman]

There is a lot of tutorials on how to backup eshop games. They also work for themes.
In small words, console-decrypt your content file and themes, then use makerom to make a CIA package. Backup done.

Thanks Chelsea_Fantasy, I'll try this!

 

[u4ick]

I like how this program doesn't actually close when i close it so i need to end the process with task manager

 

[Welcius]

Im getting an error... i think im the first one.

I can check the folders
I can create the CIA
I can install the CIA with several themes....

Yet on the menu i can only see ONE theme installed
It isnt the only one in its folder. It starts with A.

Tried twice. Second time i remade the CIA. Nothing.


Using FBI

Error: NEVER use FBI to install theme packages. Use BBM (BigBlueMenu) instead.
Solution:
Delete the installed theme package with BBM (HMMP, HMME or HMMJ) (it's the first one down Browser for US / EU / JP)

 

[Welcius]

Doesn't work for me, I am doing something wrong? I created two themes, each one with different icon/audio/preview, I install it using BBM (I hadn't installed it yet) and the icon preview and the name of my themes are fine. However when I load it fails, it doesn't apply my theme but yours of Monster Hunter instead, happens with both of my themes.

Additional info: Using an EUR cia

EDIT: Seems like maybe it is because I copied the files bgm.bcstm and body_LZ.bin from your theme, if I delete them then the program says that there aren't any themes in my folder. How do I generate those files for my theme? Thanks

EDIT2: Okay, I just realised that for making themes you need other programs as well. Yeah, probably I am blind since I didnt see that huge "How to make themes thread" sticky

 

[Ripper00420]

Used your program and everything went great. One thing, some of my icons were auto created by the checker upside down... Lol! Doesn't bother me though I will just fix later. Nice work!

--------------------- MERGED ---------------------------

I like how this program doesn't actually close when i close it so i need to end the process with task manager

I'm on Windows 10 and it closes just fine for me...

 

[gazzoose]

Hi all, I'm having an issue with this piece of software, when I try to run it (or the theme checker) all I get is a dialog stating "Failed to create empty document." and nothing more. I don't even get to see the standard GUI that I've seen in all the screenshots in this thread. I'm running Win10 x64 if that helps at all.

 

[Msama]

Is there a website where i can download themes?

 

[Msama]

I just installed a theme with FBI... :'(
Now all my games doesn't show in the home menu...

 

[aos10]

Will the themes created by this be deleted if I visited the eshop?

 

[u4ick]

Will the themes created by this be deleted if I visited the eshop?

yes will be

 

[Chelsea_Fantasy]

I like how this program doesn't actually close when i close it so i need to end the process with task manager

???
freak...
can you please upload a video showing what happen?

I will also upload you one back later...

Used your program and everything went great. One thing, some of my icons were auto created by the checker upside down... Lol! Doesn't bother me though I will just fix later. Nice work!

Can you send me the icon.smdh from these themes?

Hi all, I'm having an issue with this piece of software, when I try to run it (or the theme checker) all I get is a dialog stating "Failed to create empty document." and nothing more. I don't even get to see the standard GUI that I've seen in all the screenshots in this thread. I'm running Win10 x64 if that helps at all.

Be sure to have at least 700MB - 1GB of free space in your System Drive.
Howling Theme Tool's runtime extracts the application to:
(System Drive):\Users\(User)\AppData\Local\Temp\ir_ext_temp_(#)
Here it takes around 11MB of your HDD.
Then when you create are about to create your theme package, it creates the folder:
(System Drive):\HowlingTemps\HTT
And this temporary folder's size it's variable, by example, if you choose to create a theme package with 100 themes and all of them haves bgm, it can easily become a 500MB+ folder.
Of course, all the temporary files and folders get's deleted after the software closes.
Solution: be sure to have free space in your System Drive, usually "C:\"

Is there a website where i can download themes?

Custom: https://3dsthem.es/
Officials: Google... do not ask for them here

I just installed a theme with FBI... :'(
Now all my games doesn't show in the home menu...

I have repeated this time after time around this thread: "DO NOT USE FBI"
Use BigBlueMenu instead.
Yes FBI it's legal and do a lot of pretty stuff, but it does not haves a stable cia files control.
Please, use FBI only if you do not have any other option.

Will the themes created by this be deleted if I visited the eshop?

Yes............ but .......... you can avoid it from happening by buying the first 100 themes from your region.
Nintendo does not checks if the theme's body or content management file it's ok
It just checks if you have buy the theme or not and delete the ones you have not buyed.
Howling Theme Tool injects themes over the official ones. It edits the control file and the the containers CFA files to create a new theme package replacing the official ones.
So, the way to avoid eShop deleting your themes it's to buy 100 themes (I you will be so crazy to do this, here it's the list : )

Spoiler: JPN

蒼き雷霆ガンヴォルト ＧＶ
蒼き雷霆ガンヴォルト 七宝剣
蒼き雷霆ガンヴォルト ♪蒼の彼方
蒼き雷霆ガンヴォルト ♪霧時計
蒼き雷霆ガンヴォルト ♪碧き扉
蒼き雷霆ガンヴォルト ♪追憶の心傷
蒼き雷霆ガンヴォルト ♪灼熱の旅
蒼き雷霆ガンヴォルト ♪紅色カゲロウ
蒼き雷霆ガンヴォルト ♪月世界航路
蒼き雷霆ガンヴォルト ♪輪廻
妖怪ウォッチ ジバニャン
ファミコンシリーズ ジャンプマリオ
まるごとマリオ
まるごとルイージ
まるごとピーチ
まるごとヨッシー
キノコ・キノコ・キノコ
大きなドット ブルー×イエロー
大きなドット ピンク×グリーン
どうぶつの森 役場のしずえ
どうぶつの森 エイブルシスターズ きぬよ
どうぶつの森 エイブルシスターズ あさみ
どうぶつの森 まめきちとつぶきち
どうぶつの森 カラフルパターン
どうぶつの森 村の掲示板
ゼルダの伝説 ふたつの世界
花札 色彩
くるくるマリオ
ぐるぐるクッパ
くるくるピーチ
くるくるロゼッタ
マリオキャラクターズ 木目調プリント
マリオキャラクターズ フェルトプリント
チェッカーフラッグ ブラック×ホワイト
ボーダー ブラック×ホワイト
ドット ブラック×ホワイト
ドット ゴールド×ホワイト
スター ゴールド×ブラック
スター イエロー×パープル
ギンガムチェック アクアブルー
ストライプ ピンク×ホワイト
黒猫きょろきょろ ハロウィンバージョン
クリア ピンク×グリーン
クリア ブルー×イエロー
シンプルテーマ：オレンジ
シンプルテーマ：パープル
シンプルテーマ：スカイブルー
シンプルテーマ：グリーン
シンプルテーマ：ライムグリーン
シンプルテーマ：マゼンタ
おきらくシリーズ ファミリー集合！
脱出アドベンチャー 逢魔学園
ぶれいぶるー でふぉるめきゃら
ＭＨ４Ｇ　モンスターアイコン［狩猟の刻印］
ＭＨ４Ｇ　アイルーがオトモするニャ♪
どうぶつの森 パンプキング
ファミコンシリーズ 墓場のリンク
ゼルダの伝説 迫りくるたたかい
TOWレーヴユナイティア 黒
TOWレーヴユナイティア 茶
TOWレーヴユナイティア 焦げ茶
TOWレーヴユナイティア 金
TOWレーヴユナイティア 桃紫
TOWレーヴユナイティア 赤
TOWレーヴユナイティア 銀
クッキングママ かわいいスイーツ
マリオ キャラクターズ
マリオ アイテムズ
ピクミン みんなでお仕事
ピクミンとはらぺこチャッピー
スーパーマリオ 木製ワールド
スーパーマリオ パステルピンク
スーパーマリオ ネオングリーン
スーパーマリオ ブルー
大乱闘スマッシュブラザーズ Type2
大乱闘スマッシュブラザーズ Type3
大乱闘スマッシュブラザーズ Type4
大乱闘スマッシュブラザーズ Type1
ニャニャニャ! ネコマリオタイム
ぐんまのやぼうテーマ
ワンピース超グラバト！Ｘ特典チョッパー
ワンピース超グラバト！Ｘ特典麦わらの一味
Kawaii テーマ Vol.1
Kawaii テーマ Vol.2
どうぶつの森 CLUB 444 とたけけ
ボーダー　ブルー×ホワイト
ボーダー　レッド×ホワイト
マリオキャラクターズ　迷彩カーキ
マリオキャラクターズ　迷彩ブルー
ハテナブロック
マリオ　ひげとぼうし
ルイージ　ひげとぼうし
大きなドット イエロー×ホワイト
てれてれテレサ
まるごとクリボー
きせかえマリオ
テイルズ オブ ジ アビス
クッキングママ たのしいお料理
ポケモン おねむりピカチュウ
ポケモンゲンシグラードン・ゲンシカイオーガ

Spoiler: EUR

001 - NES Jumping Mario
002 - Completely Mario
003 - Completely Luigi
004 - Completely Peach
005 - Completely Yoshi
006 - Mighty Mushrooms
007 - Zelda: Two Worlds
008 - Hanafuda
009 - Mario Characters (Branded Wood)
010 - Mario Characters (Stamped Felt)
011 - Chess Board
012 - Stripes (Black & White)
013 - Polka Dots (Black & White)
014 - Polka Dots (Gold & White)
015 - Stars (Black & Gold)
016 - Spinner Mario
017 - Spinner Bowser
018 - Spinner Peach
019 - Spinner Rosalina
020 - Halloween: Spooky Black Cat
021 - ACNL Jack
022 - NES Halloween Link
023 - ACNL Isabelle in the Town Hall
024 - ACNL Mabel Able
025 - ACNL Sable Able
026 - ACNL Timmy & Tommy Nook
027 - ACNL Colourful Pattern
028 - ACNL Bulletin Board
029 - Polka Dots (Yellow & Blue)
030 - Dots & Stripes (Pink & Green)
031 - Stars (Purple & Yellow)
032 - Gingham (Aqua Blue)
033 - Stripes (Pink & White)
034 - nintendogs + cats Shiba
035 - nintendogs + cats French Bulldog
036 - nintendogs + cats Toy Poodle
037 - nintendogs + cats Golden Retriever
038 - Super Smash Bros. Theme 1
039 - Super Smash Bros. Theme 2
040 - Super Smash Bros. Theme 3
041 - Super Smash Bros. Theme 4
042 - Shovel Knight Launch Promo
043 - Pokémon: ONEMURI Pikachu
044 - Pokémon: Primal Groudon/Primal Kyogre
045 - Sonic Boom™: Shattered Crystal
046 - Super Mario (Pastel Pink)
047 - Super Mario (Neon Green)
048 - Super Mario (Blue)
049 - Pikmin Working Together
050 - Pikmin and a Hungry Bulborb
051 - Spotlight: Shovel Knight
052 - A Merry Mario Holiday
053 - ACNL Jingle's Toy Day
054 - Amy Rose Theme
055 - Chao Theme
056 - Shadow the Hedgehog Theme
057 - Sonic the Hedgehog Theme
058 - ACNL K.K. Slider at Club LOL
059 - Mario Characters (Green Camo)
060 - Mario Characters (Blue Camo)
061 - Polka Dots (Yellow & White)
062 - The Cat Mario Show
063 - Mario's Mighty Moustache
064 - Luigi's Mighty Moustache
065 - Tomodachi Life - Speech Bubble
066 - Stripes (Blue & White)
067 - Stripes (Red & White)
068 - METAL GEAR SOLID 3D
069 - ? Block
070 - Bountiful Boos
071 - Completely Goomba
072 - ACNL: Welcome to 2015
073 - Pokémon: Slowpoke
074 - NES Fire-Breathing Bowser
075 - Game & Watch (Colourful)
076 - Super Mario (Wooden World)
077 - Zelda: The Impending Battle
078 - Mario Characters
079 - Mario Items
080 - NES Ice Climbers
081 - NES Pit
082 - NES Donkey Kong
083 - NES Sword-swinging Link
084 - NES Samus Aran
085 - NES Balloon Fighter
086 - NES Fire Mario
087 - ACE COMBAT AH Legacy + ACES
088 - Ace Combat AH Legacy + PHOENIX
089 - Ace Combat AH Legacy + ADF-01
090 - MH4U Hunter's Seal
091 - MH4U Palicoes 4 Ever
092 - MH4U Gore & Seregios
093 - Basic (Orange)
094 - Basic (Purple)
095 - Basic (Sky Blue)
096 - Basic (Green)
097 - Basic (Lime Green)
098 - Basic (Magenta)
099 - Basic (Pink & Green)
100 - Basic (Blue & Yellow)

Spoiler: USA

001 - NES: Jumping Mario
002 - Spotlight: Mario
003 - Spotlight: Luigi
004 - Spotlight: Peach
005 - Spotlight: Yoshi
006 - Mighty Mushrooms
007 - Zelda: Two Worlds
008 - Hanafuda
009 - Mario: Wood-Burned Characters
010 - Mario: Felt-Stamped Characters
011 - Checkerboard: Black & White
012 - Stripes: Black & White
013 - Polka Dots: Black & White
014 - Polka Dots: Gold & White
015 - Stars: Gold & Black
016 - Spinner: Mario
017 - Spinner: Bowser
018 - Spinner: Peach
019 - Spinner: Rosalina
020 - Halloween: Spooky Black Cat
021 - ACNL: Jack
022 - NES: Halloween Link
023 - ACNL: Isabelle at Town Hall
024 - ACNL: Mabel Able
025 - ACNL: Sable Able
026 - ACNL: Timmy & Tommy Nook
027 - ACNL: Colorful Pattern
028 - ACNL: Bulletin Board
029 - nintendogs + cats: French B.
030 - nintendogs + cats: Toy Poodle
031 - nintendogs + cats: Golden R.
032 - Sonic Boom™: Shattered Crystal
033 - Polka Dots: Yellow & Blue
034 - Dots & Stripes: Pink & Green
035 - Stars: Yellow & Purple
036 - Gingham: Aqua Blue
037 - Diagonal Stripes: Pink & White
038 - Super Smash Bros.: Theme 2
039 - Super Smash Bros.: Theme 3
040 - Super Smash Bros.: Theme 4
041 - Super Smash Bros.: Theme 1
042 - Pokémon: Onemuri Pikachu
043 - Pokémon: Primal Groudon/Primal Kyogre
044 - Pikmin: Working Together
045 - Pikmin: A Hungry Bulborb
046 - Sonic the Hedgehog Theme
047 - Amy Rose Theme
048 - Shadow the Hedgehog Theme
049 - Chao Theme
050 - Spotlight: Shovel Knight
051 - Azure Striker GUNVOLT: Gunvolt
052 - MIGHTY GUNVOLT: Trio of Heroes
053 - Mario: Items
054 - Zelda: The Impending Battle
055 - Famicom Memories
056 - Super Mario: Wooden World
057 - Super Mario: Pastel Pink
058 - Super Mario: Neon Green
059 - Persona Q: Shadow of the Labyrinth
060 - Super Mario: Blue
061 - A Merry Mario Holiday
062 - ACNL: Jingle's Toy Day
063 - METAL GEAR SOLID 3D
064 - Mario: Characters
065 - ACNL: K.K. Slider at Club LOL
066 - ACNL: Welcome to 2015
067 - Mario: Purrfect Pals
068 - Tomodachi Life: Speech Balloon
069 - Pokémon: Slowpoke
070 - Stripes: Blue & White
071 - Stripes: Red & White
072 - Dots & Stripes: Yellow & White
073 - ? Block
074 - Bountiful Boos
075 - Spotlight: Goomba
076 - Mario: Green-Camo Characters
077 - Mario: Blue-Camo Characters
078 - Mario's Mighty Mustache
079 - Luigi's Mighty Mustache
080 - Colorful Game & Watch
081 - NES: Fire-Breathing Bowser
082 - NES: Fire Mario
083 - NES: Sword-Swinging Link
084 - Zelda: Dire Moon
085 - Zelda: Gold Edition
086 - Pokémon: Pikachu Party
087 - MH4U Gore & Seregios
088 - NES: Ice Climbers
089 - Azure Striker GUNVOLT: The Sumeragi 7
090 - NES: Donkey Kong
091 - MH4U Hunter's Seal
092 - MH4U Palicoes 4 Ever
093 - Kirby: Craft-Paper Party
094 - Kirby: Sweet Gourmet Race
095 - Kirby: Stripes and a Smile
096 - NES: Balloon Fighter
097 - Pokémon: Mega Rayquaza
098 - Pokémon Friends
099 - Pokémon Hanafuda
100 - Mario vs. Donkey Kong: Tipping Stars

 

[Hayleia]

???
Yes............ but .......... you can avoid it from happening by buying the first 100 themes from your region.
Nintendo does not checks if the theme's body or content management file it's ok
It just checks if you have buy the theme or not and delete the ones you have not buyed.
Howling Theme Tool injects themes over the official ones. It edits the control file and the the containers CFA files to create a new theme package replacing the official ones.
So, the way to avoid eShop deleting your themes it's to buy 100 themes (I you will be so crazy to do this, here it's the list : )

Spoiler: EUR

001 - NES Jumping Mario
002 - Completely Mario
003 - Completely Luigi
004 - Completely Peach
005 - Completely Yoshi
006 - Mighty Mushrooms
007 - Zelda: Two Worlds
008 - Hanafuda
009 - Mario Characters (Branded Wood)
010 - Mario Characters (Stamped Felt)
011 - Chess Board
012 - Stripes (Black & White)
013 - Polka Dots (Black & White)
014 - Polka Dots (Gold & White)
015 - Stars (Black & Gold)
016 - Spinner Mario
017 - Spinner Bowser
018 - Spinner Peach
019 - Spinner Rosalina
020 - Halloween: Spooky Black Cat
021 - ACNL Jack
022 - NES Halloween Link
023 - ACNL Isabelle in the Town Hall
024 - ACNL Mabel Able
025 - ACNL Sable Able
026 - ACNL Timmy & Tommy Nook
027 - ACNL Colourful Pattern
028 - ACNL Bulletin Board
029 - Polka Dots (Yellow & Blue)
030 - Dots & Stripes (Pink & Green)
031 - Stars (Purple & Yellow)
032 - Gingham (Aqua Blue)
033 - Stripes (Pink & White)
034 - nintendogs + cats Shiba
035 - nintendogs + cats French Bulldog
036 - nintendogs + cats Toy Poodle
037 - nintendogs + cats Golden Retriever
038 - Super Smash Bros. Theme 1
039 - Super Smash Bros. Theme 2
040 - Super Smash Bros. Theme 3
041 - Super Smash Bros. Theme 4
042 - Shovel Knight Launch Promo
043 - Pokémon: ONEMURI Pikachu
044 - Pokémon: Primal Groudon/Primal Kyogre
045 - Sonic Boom™: Shattered Crystal
046 - Super Mario (Pastel Pink)
047 - Super Mario (Neon Green)
048 - Super Mario (Blue)
049 - Pikmin Working Together
050 - Pikmin and a Hungry Bulborb
051 - Spotlight: Shovel Knight
052 - A Merry Mario Holiday
053 - ACNL Jingle's Toy Day
054 - Amy Rose Theme
055 - Chao Theme
056 - Shadow the Hedgehog Theme
057 - Sonic the Hedgehog Theme
058 - ACNL K.K. Slider at Club LOL
059 - Mario Characters (Green Camo)
060 - Mario Characters (Blue Camo)
061 - Polka Dots (Yellow & White)
062 - The Cat Mario Show
063 - Mario's Mighty Moustache
064 - Luigi's Mighty Moustache
065 - Tomodachi Life - Speech Bubble
066 - Stripes (Blue & White)
067 - Stripes (Red & White)
068 - METAL GEAR SOLID 3D
069 - ? Block
070 - Bountiful Boos
071 - Completely Goomba
072 - ACNL: Welcome to 2015
073 - Pokémon: Slowpoke
074 - NES Fire-Breathing Bowser
075 - Game & Watch (Colourful)
076 - Super Mario (Wooden World)
077 - Zelda: The Impending Battle
078 - Mario Characters
079 - Mario Items
080 - NES Ice Climbers
081 - NES Pit
082 - NES Donkey Kong
083 - NES Sword-swinging Link
084 - NES Samus Aran
085 - NES Balloon Fighter
086 - NES Fire Mario
087 - ACE COMBAT AH Legacy + ACES
088 - Ace Combat AH Legacy + PHOENIX
089 - Ace Combat AH Legacy + ADF-01
090 - MH4U Hunter's Seal
091 - MH4U Palicoes 4 Ever
092 - MH4U Gore & Seregios
093 - Basic (Orange)
094 - Basic (Purple)
095 - Basic (Sky Blue)
096 - Basic (Green)
097 - Basic (Lime Green)
098 - Basic (Magenta)
099 - Basic (Pink & Green)
100 - Basic (Blue & Yellow)

Oh, then that's why some of my themes stay even after I visit the eShop (I bought some themes). So does this also mean that if I buy the first 3 themes of that list then only make 3 themes using your tool, then visiting the eShop won't delete anything ?