Nope, definitely cia games. Could it be because I never unlinked my nands?
..Maybe? I don't fully understand how the NAND link works but that could be plausible. Perhaps @Quantumcat knows better. It's weird though because if that Nintendo 3DS folder has your save files then copypasting it over should work as is. If it doesn't then it would indicate the said files don't exist in there ..
Hindsight is 20/20 but should've backed up saves with JKSM prior to modding your console I guess to be safe if they were "important" .. Stuff like Pokemon saves etc. would be truly devastating to lose if you had spent a long time on them.