I noticed while using safeclean that it likes to nuke storage directories. It marks them as residual files and unless you are set to review actions prior to cleaning it will remove entire branches.
I have had it wipe directories I made as well as storage directories set by MEGA (MEGA.CO.NZ) file service. Forcing a redownload or at the extreme rebuild/create of work files it deemed as residual. This is one area this program suffers compared to its competitors.
Adding a whitelist ability so that you can tell it to ignore specific directories would be an amazing improvement.