The system transfer process is mostly the same as it would be done without CFW on either device, but you will need to use faketik at the end to restore any applications and games that did not come from the eShop.
What You Need
The latest release of GodMode9 (the GodMode9 .zip file)
Copy GodMode9.firm from the GodMode9 .zip to the /luma/payloads/ folder on your SD card
Copy the gm9 folder from the GodMode9 .zip to the root of your SD card
Reinsert both SD cards into their respective consoles
Section II - NAND Backup
Creating a NAND backup of both consoles is a good idea in case something goes wrong. It ensures you can recover your data in the event of an error.
For both consoles, perform the following steps:
Press and hold Start, and while holding Start, power on your device. This will launch GodMode9
Press Home to bring up the action menu
Select "Scripts..."
Select "GM9Megascript"
Select "Backup Options"
Select "SysNAND Backup"
Press A to confirm
This process will take some time
If you get an error, make sure that you have at least 1.3GB of free space on your SD card
Press A to continue
Press B to return to the main menu
Select "Exit"
Press A to relock write permissions if prompted
Press and hold R, then press Start to power off your device
Insert the console's SD card into your computer
Copy <date>_<serialnumber>_sysnand_00.bin and <date>_<serialnumber>_sysnand_00.bin.sha from /gm9/out to a safe place on your computer, then delete both files from the SD card
Reinsert the SD card into its console
Section III - System Transfer
Perform the system transfer as usual. If at all possible, choose a "PC-Based Transfer"
If you cannot follow a PC-Based Transfer and must instead use a Wireless Transfer, be aware that with this method, homebrew software, cartridge dumps, and any other data only obtainable with CFW will not be transferred over. If you choose a Wireless Transfer anyway, you will need to take extra steps to move over the lost data.Select "Do not delete" during the transfer to preserve all data on the source system, or else you will have to reobtain all lost data again by hand.
Next Steps - Branching of the Way
Were you able to perform a PC-Based Transfer in Section III?
The source console is finished. The following steps should only be performed on the target console.
Section IV - Homebrew Launcher
Launch the Download Play application
Wait until you see the Nintendo 3DS and Nintendo DS buttons
Press L + D-PAD DOWN + SELECT at the same time to open the Rosalina menu
Select "Miscellaneous options"
Select "Switch the hb. title to the current app."
Press B to continue
Press B to return to the Rosalina main menu
Press B to exit the Rosalina menu
Press HOME, then close Download Play
Launch the Download Play application
Your device should load the Homebrew Launcher
Section V - faketik
Launch faketik from the list of homebrew
If you receive the error "The External Title Database is not available.", ensure that the correct SD card is inserted into the console
Press HOME, then close Download Play
The transfer is complete! Note that you may have to unwrap all the icons that were restored by faketik.
Section IV - Homebrew File Recovery
This section will have you manually copy all homebrew files onto the target console, as wireless transfers actively refuse them.
On the target console, note all apps that should have appeared but are missing
Insert the source console's SD card into your PC, and copy the homebrew data off of it and onto your PC
Everything except the Nintendo 3DS and DCIM folders is considered homebrew data
Take out the source console's SD card but leave it out of its console, and insert the target console's SD card into your PC
Move all of the files you copied off of the source console's SD card onto the target console's SD card
Reinsert the target console's SD card into its console
Redo Finalizing Setup on the target console. This will ensure you have backups available in case the next section goes wrong
Section V - Homebrew App Recovery
This section is a work in progress. Notes:
Provide more detailed instructions on how to use ninfs.
This section will restore all games/savedata that the wireless transfer refused to copy.
Insert the source console's SD card into your PC and mount its Nintendo 3DS folder using ninfs
Copy all games/savedata that were not transferred onto the target console onto somewhere on your PC
Unmount the source console'sNintendo 3DS folder and reinsert its SD card into its console, then insert the target console's SD card into your PC
Mount the target console'sNintendo 3DS folder in ninfs, and add all obtained games/savedata into the existing contents
Unmount the Nintendo 3DS folder, but keep the target console's SD card inserted - rebuild title.db to force all the new apps to appear
Reinsert the target console's SD card into its console
The transfer is complete! Note that you may have to unwrap all the icons that were restored.