[Captain Kwok]

There's two design type designations attached to a ship. One is the external ('player') design type and the other is an internal ('AI') design type. Based on your observations, it appears when a ship is retrofit to another design type, it's internal design type doesn't get changed. Unfortunately I can't do anything about that for individual ships (only actual designs).

The AI occasionally cross-retofits, but only between the combat design types. For orders, those ships are lumped together so there wouldn't be any tangible effects as there would be specific design type orders like Troop Transports etc.