Heres a more detailed response. I've found out what file is causing this its the master file - FalloutNV.esm - being loaded after the master files have scanned for any downloaded content, and it's been reported that it has also happened on the PC version of the game too. I'm still mad that this happened and no methods of fixing it has worked for me.

No it is in two different files, we are talking about deleting from the file "Game Data" not from "Saved Game Data"

No i've found those files from the PC version of the game (which I own and has happened on it as well) which is in the the game data

And i've found this out by searching through the "ini files" directly

Just FYI... I'm continuing to look into this matter. When I have more information, I'll let you know.