Trashing prefs will likely default IO, blank the Midi Studio settings and reset several settings(which are easy to reset if you make notes of your preferred settings). Here's how I deal with some of this stuff:
Since some things get deleted when you uninstall(like to solve a big problem, or to install a newer version), so I keep a folder that is NOT in the usual place, and save copies of IO settings and Midi studio settings, along with folders with all my session templates and track presets. As for IO, because I have 4 interface(2x HD IO and 2x 192 IO) using a mix of analog and digital, I save screen shots of all the various tabs to show how each interface needs to be set for all my stuff to work. If everything gets defaulted, I can restore hardware settings by referring to the screen shots and then in the IO setup section, I can Import Settings from my saved setup from my settings folder(which may or may not match the default settings folder).
Other stuff to reset:
Color Saturation-just double-click on the colored bit at the bottom of any track in the MIX window to bring up the color settings and click the saturation button.
Auto Save-it defaults to 10 versions and every 5 minutes(change to what you prefer; I save every minute and 12 versions)
Scrolling-this will default to none(change it in the Options menu)
Other stuff- is really a personal choice, so I would just save a text file with your preferred settings so you can just run down the list after trashing prefs.
I know this seems long winded(sorry, but there's lots to cover) but once you cover your tail with some notes, screen captures and saving copies of IO and Midi Studio stuff, it only takes a few minutes to reset everything when the need arises
Last 2 cents; if you are not saving drive images, you should(and you should do this ASAP). And while you are doing that for your system drive, you also need to be backing up every session(unless you don't care if they disappear one day.....and they WILL). If you use a separate drive for sample libraries, save images of that too. Since I make my living with this, I go the last mile by cloning my system drive to a second(identical) SSD. If I have a major meltdown, I swap out the system drive for the clone and go back to work. Total downtime? About 3 minutes
