Had my P51B port flap shot off by a 109 today, while it was out 3 stages. I limped back but I had a literally uncontrollable roll. I was stuck in a dive from about 12k down to the deck. I could not stop rolling (lost 1 aileron, that might have helped) to starboard. The problem? The MISSING FLAP was still deployed about 3 stages. I had to use all my rudder and flying skills to stop a nose-down P51B going at 400mph. Well, "stop" meaning "slow down to 200mph" so I could deploy the remaining flap and limp home.
Also, if the flap is destroyed while deployed, it will remain like that at ALL SPEEDS, take note.
I just barely made it back. Wasn't fun. Felt like I lost a wingtip, in flight manerisms, until I got that other flap down again.
I'd say this is a big bug.
P.S.
If destroyed while up, they never go down. If destroyed while down, they never go up. Oversight, bug, whatever. I don't see why you're confused. Seems logical to me.