When "themeing" modules, especially core modules, as far as I know it is a good idea to take the module specific tpl.php files duplicate the ones you need and modify them once they're in the relevant theme directory.

However what if I want to modify a .inc file? Is it the same process as with tpl.php files, or is there a better workflow? Basically what I would like to do is change some of the user status messages found in user.admin.inc in the core D7 User module. But I'm not sure if editing this file directly is a good idea. Thoughts?