You can’t pick and choose which enemy units in a space you attack. If you attack one, you attack them all. The only exception is when units of a power with which you are not at war also occupy the attacked sea zone.
Does a submerged sub disrupt a convoy?
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Does a submerged sub disrupt a convoy hex?
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Yes
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Yes
though technically I believe a submarine can only be “submerged” during the combat phase and after the combat phase ends it is no longer considered “submerged”. So during any collect income phase, submarines cannot be submerged for any reason regardless at that point in a turn.
I believe Kreig has previously expressed the problems with the rule as submarines are often “submerged” regardless and it’s a misnomer.