Ha... but then, I have to confess that I used your GC again when Template mentioned it thinking it could help. So the backup file I have is the one which is wrong 
Is there any other way or will I need to reinstall it all over again ? :p And if so, is it possible to keep the save data apart and copy/past it in the new installation ?
Already damaged files can not repair with my GC...
Under these circumstances, it is probably the best solution to reinstall.
You can move the "save"-folder out of the Gamefolder, also the folder with BFE.exe and the MODs in it.
Uninstall the game and clean the registry with my
"FF7 REMOVE Regitstry Keys".
Then reinstall the game in a non-system folder and run my
"FF7 Game Converter".
Start the game, that should first call the config, so the last registry key to be set.
Now you can install other mods or start BFE.exe.
Side Note:
In the folder "BackupGC" only the files are backed up, which can also be changed by the GC.
If you want to save more files, you should do before you start BFE.exe.
@islandboy0707
have a look
here
