the option is overkill when you scan unpacked files...(not to mention the deep fix-missing option in scanner-advanced). That's based on the fact that progetto sets are 1-set-10000-pngs based...and you will run into countless file checks over and over again.
You can keep the other fix options enabled but disable fixmissing...the missing files can then be added via a rebuild of the update-sets and/or the backup folder...