Before we begin, very important note:

1. This tutorial is for firmware <=9.2
   However, if you're able to get the romfs and exefs decrypted from other sites, it'll serve your purpose.
2. The example I'm using is for Pokemon
3. If you set HANs to a different region from your 3DS, you won't be able to connect online
4. This is primarily for game-breaking patches, rather than online use.
5. Make sure you're using the newest of newest HANs, the one that allows eshop use for uses under FW10.

Other tutorials you'll need to refer to:
Decrypting and extracting CIA
Decrypting and extracting Rom


Step 1:
Decrypt and extract the Update CIA. (you can find it on a certain site, don't ask)
Make sure you extract the exefs/code.bin option and get a .code.bin file. (it is gonna be around 5312 KB)

Rename this .code.bin from the Update file as <Title ID>.code
Example: 0011C500.code

You're also going to need the extracted romfs folder from the update file.

Step 2:
Extract the romfs from the game.

Step 3:
Paste the romfs from the update file into the romfs of the game.
When it prompts, replace everything.

Step 4:
Rebuild romfs as a single file.
Name it as <Title ID>.romfs
Example: 0011C500.romfs

Step 5:
Create a hans folder on the root of your SD card.
(Example sd:/hans DO NOT TOUCH THE HANS FOLDER IN THE 3DS FOLDER)

Step 6:
Copy both the .code and .romfs file into the sd:/hans

Step 7:
Launch the game in HANs,
Set the region to be same region as your 3DS
Set the code -> SD and romfs -> SD to Yes

Proof (of sorts)

Spoiler

Don't ask me why Jeff is a female; not my cartridge.

Enjoy!
(such a pity, I wanted to connect to Korean Pokemon Wifi; probably won't work because Secureinfo mismatch)

Special thanks:
Everyone who found and exploited the exploits
Gudenaurock's Layered FS guide that gave me the idea
Asia81's tutorial allowed for me to do the test.

 

[Spatchy]

I don't believe this works with Smash Bros. I tried it with update 1.1.3 and an exception occurred when trying to run the game. There's a file in the update that is also in the base game that is significantly smaller, so when you merge the romfs folder into the base romfs folder, it makes the entirety of the folder about 500 MB smaller than it was originally. Is there a fix for this?

I don't think anyone has actually got this to work with any game... (correct me if I am wrong)

 

[Spatchy]

just an update: smea has said that the hans included *hax 2.7 will now work with updates so no one will have to do any of this!

"so hax 2.7 was supposed to be up yesterday but then i figured i'd try to get updates working in HANS and now i dont know when i'll be done"
"just a heads up, games with updates should be able to run fine in HANS but wont let you return to hbmenu; keycombo will return to home menu"

 

[Sonansune]

just an update: smea has said that the hans included *hax 2.7 will now work with updates so no one will have to do any of this!

"so hax 2.7 was supposed to be up yesterday but then i figured i'd try to get updates working in HANS and now i dont know when i'll be done"
"just a heads up, games with updates should be able to run fine in HANS but wont let you return to hbmenu; keycombo will return to home menu"

good

 

[caspaas]

I have a Rutile Ruby ROMFS
but I cant seem to get online.
It keeps wanting me to update to 1.4
I thought HANS was suppose to work with updates installed?

Or am I not doing this correctly?
Please help me

 

[RankouOTN]

Anyone get this to work with Fire Emblem Awakening DLC? I've had no luck, and I have no idea how to get any of this to work.

 

[Gaming796]

If anyone can help me out with this..... Can anyone please get a Mario Kart 7 Update CIA? 'Cause I'm on 11.0.0.-33 U Firmware so I can't even dump the update data as a CIA. If anyone has a 4.1 - 4.5 Firmware on their 3DS, please download the Ver. 1.1 Update from the eShop and follow this tutorial to dump it as a CIA. After that, if you can provide a Download link of the CIA to me, it will be of great help.....

 

[Merch]

Is there any way I can get a decrypted Smash Bros. 1.1.6 USA Update .cia? I checked on that ISO site & that CHAOS site, & nothing seemed to pop up. Even tried decrypting the update via the Hacking Toolkit, & all of the files never decrypted for me; probably due to the fact that it's untouched. I'm asking for this, because when I had rebuilt my Smash 3DS romFS for all of my mods, it was on the base firmware, & Bayonetta/Kamui happened to be in the mix, so it never ended up working properly, & as we all know, all the DLC came after a different update than the base update. If anything, can someone PM me a decrypted version of the 1.1.6 update so I can rebuild the romFS again to use the 1.1.6 update? If needed, you can PM me on that ISO site, that CHAOS site, or here; usernames are all the same like the one on this site. Thanks in advance.

 

[botik]

Step 3:
Paste the romfs from the update file into the romfs of the game.
When it prompts, replace everything.

In general, this does not work.

game romfs is not overwritten with the romfs of the patch, but merged or mixed
"aaa"(game) + "bbb"(patch) not equal "bbb" in fact equals "aaabbb"
Is there a way that mixes romfs(game + update)?

P.S.
For Nintendo Switch there is a way. On emulator Ryujinx or Yuzu there is a possibility create one dump romfs (game + patch + DLC)
On emulator Citra for 3ds game you can't do it