Well yes, there is a sequence to the turn, and the surprise strike is a specific part of the Combat phase (taking place towards the start of it) but I meant in the case of removing casualties sequentially (as in, one after the other. As in, the removal of one affects the remainder) after the attacker has rolled his hit dice. If this is how removing casualties occur and and a unit can go from ineligible to the eligible in the same round then this is the scenario:
1 sub, 2 fighter, 2 tacs VS 2 fighters, 1 dest, 1 transport on defense. Attacker scores 3 hits (2 aircraft, 1 from sub)
If I am the defender, as the first casualty from the one of the aircraft hits (any defending unit can be removed except the transport) I choose the destroyer. As the second casualty (from one of the aircraft), I choose one of the fighters. The only unallocated hit is the sub (and this hit must be allocated if possible). With the removal of the destroyer (because remember, it is sequential, the destroyer is dead before the sub casualty is removed and units can go from ineligible to be hit to eligible to be hit), the transport is now the only eligible target for the sub and is removed as a casualty. I haven’t negated the hit or cancelled it (that would be against the rules for maximizing hits). The transport isn’t defenseless as there are still friendly units in the same zone that aren’t other transports (that can fight and there are attacking units present that can still kill it and be killed by it) and the transport is an active participant in the combat (per pg 19) that can only be taken as a casualty if there are no other eligible units.
As for your example, that lends weight to what I am saying, though the outcome is the same. If you scored 4 hits but the transport remained ineligible (thus the 4th hit was negated), for example, then everything else is dead, the transport falls under the Defenseless Transport rule and is removed automatically regardless.
EDIT: I have the dumbs, can’t word