Well, sheesh, the only thing a Kindle factory reset touches anyway is the userstore!
Surely your logic requires you to reflash the firmware... to a read-only partition...
Anyway, it's not hard to find all non-packaged files on a linux OS, and confirm their integrity. You can even version-control them, to be really sure.
There are plenty of tricks, and failing that, grounds for optimism, for avoiding extraneous HDD reimaging.