Ok did some tests in windows 8.1 virtualbox. Yes indeed, the cleaner does wipe out the mozilla profile and all what's involved. Windows still boot after the cleanup. As for the windows update files, not sure but I am afraid of what else it has deleted.Wise now change to a new version 8.39. Hopefully that will fix all this.
I can't imagine all the damage it has done to users who use 8.38. That could strike a dead blow to the cleaner if it so unreliable and destructive. How can the company did not get that before the release. You are playing with important files here so it has to be 100% bullet proof.
EDIT 8.39 seems to be all right but my confidence has been shaken.