Rule #1 - Always back up everything on your computer. Then WHEN your hard drive fails (because it WILL fail someday) you already have a backup and can pick up where you left off.
Adding covers is pretty simple and if you re-convert the book even in the same format the cover gets changed without changing anything else.
What else about your books is messed up that you want to fix?
Completely re-installing should always be your last choice for any system.