we have a user that was removed then re-added to active directory. during this time his My Site was marked for deletion. Is there a way to set a flag to remove his profile from the My Site clean-up timer job?
You cannot unmark a MySite for deletion as far as I know. What you can do is to take a backup of the site collection and restore it after it is deleted.
Once the profile is marked for deletion, the flag is set in the UserProfile_Full table and then the MySite Deletion table is updated with the information to delete the MySite on the scheduled date. The schedule has started, so without some sort of highly unsupported (and highly un-recommended) way to stop this, wait for the deletion and do the restore as this is the only option.