If you can't lock on a target any further it's dead - but maybe still floating or in your case flying. It should sink or crash later, without further interaction and count for your patrol report.
There are reports of unlockable targets that don't sink and don't count in your statistics either. This may be a bug.
Personally I think it may be possible to shoot the hitpoints down to exactly 0 (zero) - resulting in no negative damage to destroy the target, keeping it functional - but with 0 hitpoints not recognizable as valid target for the game.
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