Restoring apps after a transfer

Did a system transfer last night from my modded N2DSXL to my modded N3DSXL since the former has been having some hardware issues.

I made a backup of the contents of the SD card from the 2DS beforehand so that I could theoretically access all of my apps again.

When I reformatted the SD card and restored the backup, all of the installed apps were gone, but their data is still on the SD card. Annoyingly this includes stuff like FBI (but I can boot into Luma and GM9 as normal).

Is there any way to restore the apps that I had installed? It’s not the end of the world if not, but I’d rather have as minimal faff as possible