From the message below in Setup Wizard, I don't understand what "changes" could be disabled temporarily as damages had been done.

"Safe mode link: It is a good idea to bookmark this link to the safe-mode version. If a major problem develops when customising your site it disable your changes temporarily. In the rare event that you need the link, note that it only works when logged in as a super-administrator."

Safe Mode will ignore anything in a *_custom folder, which includes (basically) themes, your Comcode pages, overridding changes to default pages, non-bundled addons.