I did some, erm, target practice, with a test-savegame Commander in a maxxed-out Juggernaut plutonium ass, onto a, hm, GalCop station. It was full of trumbles! That's why I did it!
Anyways, after some time the station started to went plasma and the missile lock went away - "target lost" was messaged every shot - but then the target reactivated.
I think the entities this happens with are being made indestructible by actually being destroyed (1 rank awarded) and being respawned immediately in the same position, but with the same energy low as before!
So, every further shot destroys the entity again, awarding 1 rank, respawning the entity with nearly no energy, and so on.
Why this can supposedly happen with no-main station entities no idea, but perhaps this respawning could also bring indestructible entities back to full energy?
Another solution could be to have no indestructible entities in the game, just very difficult ones. Can't see where the problem would be with a main station with energy 100.000 and 100 energy recharge rate.

L