What would happen if I didn't have a blank database and upload/ unpack all of my files in the root -- then rewrite over top all the existing files. Would this break Joomla?
Technically, things should be fine...BUT, if you have anything that's a hacked file or added file that's a security issue, it would be deleted if you delete everything first then unpack all your files.
If you're restoring a site, I would restore it from scratch first in an empty directory, or directory where the other directories and files there don't conflict with any of your site's, then do any updates or changes after it's up and running.