Raccoons, files and challenges reset

I'm on my second play of re9 and I've just loaded the game up to find that I have apparently completed no challenges, collected no files or destroyed any raccoons despite being almost done with most of them. My save data is still there but my CP is reset and no collectables have saved. I'm about 4 hours into my second play, trying to do a 100% insanity run and REALLY don't wanna restart. Anyone got any ideas ??