I was experimenting with my debug rom. I didn't save or anything. I reseted it and what do you know? File 1 said LINK when it was supposed to say Link. I reseted again. File 2 was erased and File 1 said LINK. BTW I had all the medallions but no spiritual stones and I had 14 hearts. Weird.
I opened my regular rom and everything was gone.
I went into the Project64 saves and found out I still had the save.
Either the Debug Rom corrupted the save or made it so that I can't read it. Either way, I deleted it (the debug rom).