Subs can still be ignored, unless they’re attacked.
That doesn’t make sense from the way the text was updated. Here is the original paragraph:
Step 3. Land Combat: If the sea zone has been cleared of all defending enemy warships except submarines and transports,
and the attacker still has land units committed to the coastal territory, move all attacking and defending units to the battle
board and conduct combat using the general combat rules (on the next page). Remember to put casualties from bombardment
(if any) in the casualty zone.
Here is the updated faq version:
Page 17, Amphibious Assaults - Step 3. Land Combat: The first sentence should read: “If there was no sea battle or the sea zone has been cleared of all defending enemy units except transports and submerged submarines, and the attacker still has land units committed to the coastal territory, move all attacking and defending units to the battle board and conduct combat using the general combat rules (on the next page).”
“submerged” was added and in italics. It seems to me that, submerged subs can still be ignored, but not ones that decide to fight.