Character level and challenge reset

I’m having a weird issue: after playing for an hour and then relaunching the game to play some more, my character resets—along with the challenges I completed and my trader progress. I thought it might be a corrupted save file, so I restored a save from an hour earlier, played normally for another hour, quit the game, and the exact same thing happened again. The problem is that it only happens after some time, not immediately. I knew you couldn't trust mods—if they don't break the game right away, they'll do it eventually.