Hi, I demonstrate indesign for education a lot, and I am also experimenting with a lot of different mixes of settings, such as type and composition options, units and increments etc, lots of things. Some workshops I am doing will mean that I will have to trash/reset the preference files a lot with the SHIFT>CTRL>OPTION>COMMAND Mac keyboard sequence on startup, like 8 times a day for a week or so between multiple 101 sessions on my machine. Other than me having to reenter my favourites at the end of the session, can it damage my installation of Indesign at all doing this so much?
It shouldn't hurt anything to use Restore Preferences often. However, I'd keep a copy of your preferences to restore them (to save time). This article explains the file which are changed when restoring preferences: