Found it! And I ended up doing just that. Because the files aren't named, I had assumed that the system transfer included some important system-sd-pairing that shouldn't be tampered with. Guess not.
Backed it up and tried simply replacing the 2DS 2ca900d83112b5323030303000284245 folder with the 3DS fa2d00ac4760a300534430320002544d folder which apparently has my digital game save files. The folder I removed was about .3gb larger though, I wonder what I'm missing lol. Thanks for joining me in this little adventure.
Glad you were able to figure things out. You probably are missing something there though, did you keep that back-up? You never know.
(If I'm not mistaken you should be able to match up files if you think it's worth the effort, so I guess you could add save files that are missing on your other sd card if you want to. It's a bit of a gamble tho, those file names aren't easy to figure out.)
I don't think the FE4 patch has progressed much since 2007, and the FE5 one since 2008 or 2009. Perhaps someone else has picked up the project, but I wouldn't wait if you are interested in the games. Pretty sure the main stories are finished, plus the translation related to actual gameplay. You might be missing some support convos and things like that, but it has been years since I played FE4, and I never finished 5.
I don't know about FE5, but I just took a look and it seems like FE4 has a more up-to-date patch actually. This one hasn't been finished either tho.
http://serenesforest.net/forums/index.php?showtopic=39994