At first glance they may be using a custom excerpt function, and the hook may not be firing. I would check to see if there are any hooks in their function you can use.
Theme files will be unaffected, it is core files that will change (Anything in the wp-admin and wp-includes directories). If there are modified core files you need to:
1) Never use that contractor again, and
2) figure out what modifications have been made so they can be rewritten to work with the new version.