I don’t have the other system I made the CTRNAND on.

 

That video tutorial guide is the improper method of doing a System Transfer between two 3DS systems with custom firmware. Bypassing the official Nintendo method of System Transfer carries the risk of banning both the (source) Zelda n2DSXL and (target) SNES n3DSXL.

The proper method of sharing games and saves between CFW 3DS systems involving official System Transfer:

• 3DS system transfer today- Whats the best way?
• CFW to CFW system transfer

***

I re-read your first post. You mentioned you deleted the Nintendo 3DS folder off the SD card. That folder contained all your games, saves, and extdata. You just made it infinitely harder to retrieve your lost data on the card by having to use a data recovery software. Check this post for program options; I recommend EaseUS Data Recovery Wizard (look around the Internet).

 

The ctrtransfer.bin you made in Decrypt9WIP from the Zelda n2DSXL contains all the files from its [1:] SYSNAND CTRNAND.

Despite what that video tutorial told you, performing these actions:

• GodMode9 → 0:/.../ctrtransfer.bin → CTRNAND options... → Transfer image to CTRNAND → Transfer to SysNAND → etc.

does not restore the target system's personal files tied to your Nintendo 3DS folder onto your source system (SNES n3DSXL).

These would be the:

• [certs / import / ticket / title / tmp_i / tmp_t] *.db files
• LocalFriendCodeSeed_B
• movable.sed
• SecureInfo_B
• HWCAL0.DAt
• HWCAL1.DAt

The most important file from the set is the movable.sed; without this you cannot decrypt data in the Nintendo 3DS folder and make backups of everything. Luckily for you, you can perform a variant of an unauthorized System Transfer to retrieve your titles as *.cia and game progresses. The ctrtransfer.bin does contain those files, but you'll need to follow a different procedure than the video guide to get it running.

The n3DSXL must be kept offline at all times while you go about backing up everything. Failure to heed this advice can get both your SNES n3DSXL and buyer's Zelda n2DSXL banned from Nintendo online services.

Please read and familiarize yourself with this recently made post guide. Study the techniques involved and understand the process.

• (Very Bad Tutorial) Perform an unauthorized System Transfer

I can write a mini guide in terms of how to go about using the ctrtransfer.bin to pull it off. Just know that you'll need to remove and discontinue using your old n2DSXL profile on the n3DSXL once all the games, DLCs, updates, saves, and extdata are retrieved.

 

(Very Bad Tutorial) Perform a *simplified* unauthorized System Transfer with a privately dumped ctrtransfer.bin.

Do not attempt this unless this is for data recovery.​

Key Notes
1 - This tutorial is an offshoot of (Very Bad Tutorial) Perform an unauthorized System Transfer.
2 - Any 3DS user who is using this guide is assumed the following:

• Has read the former guide in detail and thereby knows how to do certain actions and techniques in GodMode9, Decrypt9WIP, Checkpoint, etc.
  
• Understands the inherit risk of performing a homebrew System Transfer not officially sanctioned by Nintendo (ie, online service bans).
• Understands the risk with modifying CTRNAND files, especially the SysNAND (ie, softbrick without a NAND *.bin image to recover from).
• Intends to perform this procedure for the express purpose of backing up and recovering games, DLCs, updates, saves, and/or extdata.
• Will remove and delete the donor NAND image once all sought out data is retrieved; will make a new user profile with the 3DS system's native NAND image.

3 - Because this guide is simplified, there are certain procedures not included:

• Checking the source system's SD card.
  
• Making a EmuNAND setup.
• Updating the source system's 3DS firmware and custom firmware.
  
• Updating the target system's 3DS firmware until later.

You will need the following

• Two (2) 3DS systems of the same series.
  • old & old: o2DS, o3DS, o3DSXL
  • new & new: n3DS, n3DSXL, n2DSXL

• SD card from the designated source system.

• 4 GB or larger SD card for the target system.

For this example, we will designate:

• Source System: n2DSXL
  • Source Card: (A)
• Target System: n3DSXL
  • Target Card: (B)
• n2DSXL | n3DSXL | (micro) SD cards

Section I - Dump the ctrtransfer.bin from the source system (n2DSXL)
Use the n2DSXL and its micro SD card (A). Let's assume card (A) is a 128 GB PNY micro SD card with 90 GB of installed data in the Nintendo 3DS folder.

1A. GodMode9 → [S:] SYSNAND VIRTUAL → ctrnand_full.bin → Copy to 0:/gm9/out.​

or

1B. Decrypt9WIP → SysNAND Options → CTRTransfer... → Dump transferable CTRNAND → etc.​

Possible output names include:

• ctrtransfer.bin
• XX########_ctrtransfer.bin
• ctrtransfer_sys.bin
  
• sysctrtransfer.bin

​

For convenience, any further mentioning of the CTRTransfer image will be referred as ctrtransfer.bin.

2. Turn off the n2DSXL and remove card (A). On a computer, download seeddb.bin found here. This will be needed for offline seed importing and decryption for a later section. Place this file on card (A) at:

• sdmc:/gm9/support/seeddb.bin

​

Section II - Prepare the target system's SD card (B)
Let's assume card (B) is a 16 GB SanDisk micro SD card that contains nothing of value.

3. Reformat card (B) as FAT32 + 32 KB cluster size with Windows File Explorer or guiformat.​

4. Do a full Write + Verify Test on the empty card (B) with H2testw.

• If the card fails hardware inspection, you must replace it and go back to step 3.

5. Build a test custom firmware setup using the starter kit archive found here.​

Section III - Review the target system (n3DSXL)
Update the custom firmware and 3DS firmware on the n3DSXL. At the time of writing (Nov-26, 2018), the latest trifecta custom firmware includes Luma3DS v9.1, boot9strap v1.3, and GodMode9 v1.7.1, and the latest version 3DS firmware is 11.8.0-41. If the target system has Luma3DS v7.0.5 or older (arm9loaderhax), follow this guide instead: A9LH to B9S.

6. SafeB9SInstaller → <Left> <Down> <Right> <Up> <A>. This will update boot9strap.

7. GodMode9 → (HOME) → Scripts... → GM9Megascript → Scripts from Plailect's Guide → Setup Luma3DS to CTRNAND.

○ For a cleaner Luma3DS chainloader setup, delete any unwanted *.firm payloads at:

• 0:/luma/payloads (SD card)
  
• 1:/rw/luma/payloads (SysNAND CTRNAND)

​

8. Luma3DS v9.1 configuration (with SD card and without SD card), select only this option as the default:

• (x) Show NAND or user string in System Settings

9. System Settings → Other Settings → System Update to update the 3DS firmware to Sys 11.8.0-41U.

10. Turn off the n3DSXL's WiFi and keep it turned off at all times.

• HOME Menu → HOME Menu Design → Wireless Communication / NFC: OFF.

or

• Rosalina menu → System configuration... → Toggle wireless.

11. Backup the n3DSXL SysNAND *.bin image.

• GodMode9 → (HOME) → Scripts... → NANDManager → <X> Backup SysNAND → etc.

12. Turn off the n3DSXL and remove card (B).​

If you're wondering why you're not using card (A) for Section III, that's because H2testw testing was skipped on it. If card (A) happens to be fake or faulty, you eliminate the risk of being unable to recover from softbricking the target system (n3DSXL) by offloading its NAND *.bin image to a known to be tested good card (B).


Section IV - Implant the donor NAND image

13. Insert card (A) into the n3DSXL and boot to GodMode9.​

14. Enter the [1:] SYSNAND CTRNAND directory. Hold the L-shoulder button and press right (d-pad) to highlight everything in yellow. Let go of the L-shoulder button. Press (X) → <A> yes → button combo to delete everything. Once prompted, relock the write permissions.​

15. 0:/.../ctrtransfer.bin → CTRNAND options... → Mount image to drive. You should now be in the drive [7:] FAT IMAGE.​

16. Hold the L-shoulder button and press right (d-pad) to highlight everything in yellow. Let go of the L-shoulder button. Press (Y) to [CLIPBOARD] select everything.​

17. Back out with (B) button, and go back to the [1:] SYSNAND CTRNAND directory. Press (Y) → Copy path(s).​

18. In [root], highlight white the [1:] SYSNAND CTRNAND. Hold the R-shoulder button and press (A) → Fix CMACs for drive → <A> yes → button combo.​

Section V - Backup the game saves and extdata

19. Unplug the Internet router in the house and any known sources of Internet you had previously setup on the n2DSXL.​

20. Boot the n3DSXL to HOME Menu and quickly access Rosalina menu. Turn off the WiFi in case it turns on.​

21. Don't get comfortable seeing your collection of games. With either Checkpoint or JKSM save manager, backup all your game saves and extdata.​

Section VI - Dump the titles as CIA files
Before you start, this would be good time to mention again adding the recommended seeddb.bin from step 2 if you missed it before. While it's not strictly needed, it'll save you the headache determining which games require seed later down the line.

22. Dump all your games, DLCs, and updates as *.cia using Build CIA (standard) in GodMode9.

• GodMode9 Usage - Dumping a Title

​

Archiving 90 GB worth of data for card (A) with a usable capacity of ~120 GB [for an 128 SD card] means there would be 30 GB of working free space. This will require 3 to 4 sessions of backing up and copying the files between card and computer.

Another approach would be splitting the title subfolders into two half sets found at:

• sdmc:/Nintendo 3DS/<ID0>/<ID1>/title/00040000/00XXXX00

This would reduce the number of sessions to two attempts. Either route requires keeping track what has and hasn't been backed up.

23. Once everything has been backed up, turn off the n3DSXL and remove the card (A). Delete the no longer needed Nintendo 3DS folder on the card.​

Section VII - Restore the target system's original NAND; remove the illegitimate System Transfer

24. Insert card (B) into the n3DSXL.​

25. GodMode9 → (HOME) → Scripts... → NANDManager → <R> Restore SysNAND (Safe) → etc.

• This will remove all the private files sourced from the ctrtransfer.bin that has the n2DSXL identity.
• This will restore the n3DSXL actual identity. If you wish to further verify this yourself, go to:
  • 1:rw/sys/SecureInfo_B → Show in Hexeditor to look for matching serial number at the end (XX########).

26. Turn off the n3DSXL and remove card (B).​

***

Edit - Before moving onto step 27, you may want to consider reformatting a 128 GB or larger capacity SD card in FAT32 + 64 KB cluster size. This can help a little with loading times. It also wouldn't hurt to now check card (A) under H2tesw.

***

Section VIII - Fresh start for the target system (n3DSXL)

27. Reinstall all the *.cia titles. Restore the saves and extdata. Once everything is how you like it to be, backup the SysNAND that's now inclusive of your tickets, etc.
​