Oy, this happened to me a few months back and what triggered it was me opening steam and doing things there. It ended up cooking my normal game that I play from an OG game copy, nixing my cdkey, like what happened to you. I don't know what Steam does when you open it, but it changed stuff in my normal game folders. I had to google it and get into the registry to update the key code like you did. I saw someone talking about locking folders so they couldn't be overwritten by other programs, but perhaps that'd screw up playing the game normally, because it'd need to be written to then as well. I don't know, I'm just not wanting to open Steam now to do anything because it screwed my game up so much. When I fixed it, modded stuff came all back, but the normal stuff didn't return. I could upload a backup I have somewhere of my stuff, but I just don't play much on non-modded servers. Glad you figured it out Raisin!