Ships in orbit around defector planets will become disabled. They show they still belong to "someone" but they cannot be controlled. They will defend the planet. I say "someone" because at least once, a Yor planet defected to the Krynn (me) but was the ship flagged Iridium.
Steps to recreate: Influence capture a planet with a defending fleet. (Sorry but my save game failed to exist after saving. Don't know who's screw up that was.)