> I ran CMP up against my sets yesterday using MAME79u4 exe.
>
> As usual, CMP wanted to delete some files (Area51 bits, for example).
>
> But later, I checked my Backup and it's empty.
>
> I didn't change any settings and Backup always worked in the past.
>
> Is there a setting under 'Advanced' I should check?


No.
Well...only real unneeded files will be backuped. Wrong placed files will be moved to the correct place via the backupfolder but won't stay there. The backup option works fine for real removed unneeded sets.

Roman Scherzer
ClrMamePro