You can make a backup of your CATSettings directory.
If you have admin access, you can edit your environment file and add a second (or third or fourth) directory to the CATReferenceSettingsPath variable for your personal "permanent" settings. Settings in this directory are not modifiable unless you are running CATIA in Admin Mode.
Then, when you have everything set up just the way you want them, exit CATIA and move the contents of your CATSettings directory to the one you specified in your CATReferenceSettingsPath. Now, if your personal settings get messed up, nuke them and you will be back to the ones you set in the CATReferenceSettingsPath directories.