I was editing a mod called "DC Mini Expansion" I was working on and I noticed that I suddenly and randomly had 5 coppies of the mod entiled DC Mini Expansion (2), DC Mini Expansion (3)... Upon further inspection these new copies turned out to be other mods but renamed. Even further inspection lead me to finding that not only were many mod's names mixed up, but an ESM and several readme's as well. I deleated DC Mini Expansion after and began cleanup. Once I was done I tried to put it back into the folder only to have to get rid of it now under the name: "Fallout 3 Tactics". As a precaution now DC Mini Expansion is now destroyed. I am not going to work on the GECk in a bit either because I am not 100% sure if that wasn't that.
So in short it seems that many of the names of things (not just mods now I notice) in my Fallout 3 Data folder have been switched arround without my knowlage as to how, when or why. Any knowlage as to what the hell just happened would be nice.