I recently bought a used old 3ds from gamestop. I installed over 50 cia files and I wanted to know if there was anyway to transfer my games to a 3ds xl flashed obviously, thank you guys.
Well, you can't transfer the EmuNAND, period. At least, not with the knowledge we have right now. Each 3DS uses a unique key to access its NAND; one 3DS' emuNAND won't work on another. As for the GAMES... if you have a way to install CIAs on the target 3DS, and you still HAVE the CIAs, you might be able to manage it by copying the folders from one 3DS's SD card to the other, but you'd still need to use FBI to "reinstall" all the CIAs (use SocketPunch over the network - much easier) because otherwise they don't have tickets and the 3DS will refuse to run them, even under rxTools. Telling FBI to reinstall them should give you a "software already installed" error or some-such, but the important part is that in doing so, it creates a ticket. Warning: I'm not /sure/ this will work. It might. Try it with a title or two and see, assuming you do still have the CIAs.
You won't be able to transfer any unsigned cia. You'll have to reinstall all the cia games on your other 3DS. You can backup the saves with SaveDataFiler then import them on your other 3DS. You must create a save file from each game before you can import, remember that.