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So it is better not to attack an territory with the special submarine attack, before you do an amphibious attack on the same territory, because "unfortunately" you could destroy all opposing units and are not allowed to continue with your amphibious attack.
Is it correct what I am saying?
It depends on the number of defending troops but yes it can be a risk but you should only ever play it wrong once.
Is it not a disadvantage in the game that you cannot attack empty territories?
No. If anything its just another beautiful part of a fantastic design.
Experienced players purposefully leave pockets of empty space inside their territory to delay an opponent's advance.