Using those preferences shouldn’t do anything to the files in your Resource Tree, they just clean the caches.
I have those settings enabled and have never experienced anything like that so if that’s what has happened then I would bet it’s something else that caused it.
Also your image is showing loads of objects in the Resource Tree, and I’m assuming this was screenshotted after your issue appeared as it seems odd you’d have a picture of these settings before anything happened?
This is probably unrelated, but why are you using such an old version and not updating to the latest?