Perhaps Starfleet revokes the commissions of all its retiring officers? Or perhaps revoking of commission was to be punishment for Kirk and his team (although apparently not followed through since the heroes still have their uniforms in ST:GEN).
I don't think that's the case. In ST:TMP, we get McCoy complaining about his "reserve activation clause". He was essentially re-instated at his previous commission.
Also, we see Kirk, Scott, and Chekov in uniform at the beginning of Generations. Presumably that means they haven't been decommissioned, and are still on active service, or maybe in a reserve role.