if (most of) your save files are fine, it's likely your gamedata.dat is corrupted. (i don't mean what you mentioned, i mean the files that correspond to the save slots, for example, slot 1 being sonic & tails with all emeralds and being in arid canyon.) files that correspond to amy, fang, and metal will be missing though if the gamedata.dat is broken due to them no longer being unlocked.
you could edit it to be back exactly as it was with some complicated coding shenanigans but you're better off replacing it with a 100% one or just starting from scratch (depending on your opinion of wether downloading a save is "cheating" or not, i suppose).
if your save slot files are gone too then it could be a different problem entirely.
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- Edit: if your save select screen looks anything like this
View attachment 77057
it is in fact your gamedata.dat
(the "can't load" files are files corresponding to Amy, Fang, and Metal)
that being said i have no idea if you had a Fang, Amy, or Metal save in the first place so maybe this info is useless to you. i'm just trying my best.