Here's how you do it (it took me a minute to figure out, which, given that I did a ton of online testing for this game, means it was ridiculously obtuse):
1. Log in as the manager in question (the Commish password lets you log in as any GM).
2. On the Manager Options screen, check Play in Commissioner Mode (again, you'll need to enter the Commish password to do this).
3. From the Manager menu, select the Available Jobs screen.
4. Click on "Apply as GM" for the franchise you wish him to (resume) running. The "application" will be accepted automatically/instantly.
5. Once he's assigned to the team, go back to the Manager Options screen and uncheck Play in Commissioner Mode so that he doesn't try to usurp your power in a season or two.
Sorry we didn't come up with a solution for this in time to help you!
- Kai