AFAIK, the percentage of mission completion doesn't matter in TWoS: it's all date controlled, meaning that when you reach the end date, the mission is over and other missions will appear.
Just be sure NOT to be in the bunker during the end date of the last campaign mission, but in open sea, else you may not transfer correctly to the next campaign chapter. Read the TWoS threat about that, and other tons of advices and HowTos.
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