I wasn't talking about save data. I was talking about game backups. Basically, there are two ways in which backups can be handled: Either it's installed or it's not.
For the 3DS, the .CIA files have to be installed meaning there is a limit to how many games can be installed and it's very inconvenient to move them. On the other hand, there are the .3DS files and .3DSX files which basically act like a ROM file. A disc image to be mounted, which pretends to be a game cart.
For the Switch, the NSP files are used for installation while the XCI files are for disc image mounting.
I don't consider installed games to be viable long term for any console. If a console breaks it has to be reinstalled, if you run out of space you have to uninstall, etc. [1] Once emulators come out it's even more annoying. For example: While emulators like Citra can run games that were installed, you have to go through the processing of dumping them from the 3DS, whereas if you kept them as .3DS files it would just work.
What I want to do is play my game backups without installing them as CIA on my N3DS. I don't really have a problem with the idea of converting saves (even if it would be time consuming) nor do I have an issue with converting backup file types, but I do want the latest firmware version to play online again or at least to be able to buy and play the latest games offline.[2]
It's nice to know that Luma3DS can run a Gateway emuNAND, but if it can't do anything more than run .CIA files it's an inferior product. It is possible for CFW to access the Gateway SD card, so the fact that no one seems interested in adding .3DS file support is rather strange to me.
For moving the emuNAND to the 3DS that's a nice idea for cloning the emuNAND onto a new 3DS at the very least.
Well, since my games are legit backups, and since Nintendo has new ways of detecting piracy, I'd rather not even give the appearance of being a pirate. Nintendo would be able to see that I don't own the eShop version of my games very easily, whereas my carts each have their own legit and unique header so no problem running them as backups.
I wouldn't be surprised if everyone who switched to .CIA to go online gets hit with a bulk ban, since Nintendo is fond of doing it that way. To the best of my knowledge no one has been banned yet, but Nintendo clearly is planning something and will probably time it around a new release. This will likely result in the community finally accepting the need for emuNAND for homebrew and proper backups in it's CFW.
[1] - Not entirely true on the 3DS
[2] - So, your end goal is to use a different 3DS than the one you use Gateway on, have it on the latest firmware and be able to play games backups without installing them? If so, then the answer is simple. You cannot do that. Gateway will simply not work on 11.9.