There are 2 kinds of flashcards: those that do accurate card emulation (Sky - and therefore require signed roms, unless the console is modded in the first place), and those that are a random piece of hardware requiring proprietary drivers (Gateway and clones)
In either case you need to have CFW in the first place, and there are already not one but two formats that can be used to run homebrew on CFW
(Nothing forbids you from trying to convert RetroCrap.cia to RetroCrap.3ds - the newest versions of makerom have such a feature - but results are not guaranteed)
Oh, you're doing this for the saves? Then you will definitely need to mod the emulators (in the source code) to adapt them from loading arbitrary files on the console's SD to roms from their romfs and saves to a standard 3DS save (the latter part has never been done in any homebrew, to the best of my knowledge)
For starters, RA has been broken for quite some time and newer versions don't even boot. Not to mention that homebrew doesn't like running from flashcarts, and gateway needs an emunand anyways, so it isn't worth it for transferring saves.