[Fisneaky]

Don't think its the "fixer". Running the version installed in my Il2 root folder gave no errors after pasting in my backup.

Backup your filelist every time (and check the size before and after).

Another way is to copy your filelist.txt to a new Temp folder and extract the mods there.
Backup your old filelist.txt and paste all the new stuff across to IL2 folder.