If in a sea combat the defending submarine survives and destroys the attacking destroyer the transport may not unload, because the attacker failed to clear the seazone from enemy units. The attacker would most likely retreat his transport, then.
Actualy if there was a sea combat it would continue untill there is only 1 side left in the combat.
You cannot ignore the sub halfway through the combat, you either ignore it or you dont. So in your example the transport MUST retreat or be sunk and therefore can never be near the intended landing zone. Unless the sub player submerges but why would anyone ever do that.
Sure, I did not say anything else. This situation is not a situation about ignoring submarines, after the first round of combat is over and the attacking destroyer has been destroyed. I talked about retreating, not about ignoring, then.
This situation is a situation where the attacker decides to retreat or not, following the retreat rules.
Most likely the attacker (transport) would retreat, for the reason you described.