Well, of course you could use a text-comparison software for such purpose. The only thing we sometimes update a lot of stuff ;-) So you could keep a lot of time tracking all changes. I hope with miniBB we've achieved that you may have a lot of custom additions WITHOUT modifying the core files. Then you could just overwrite updated files and save a lot of time... at least this is what I'm doing in my practice.
But if you have modified .PHP core files, well... it makes the things more complicated, and only you become responsible here ;-)