To answer the original question for anyone coming along later;
i can also choose a bow gun to replace the stern gun... but its still a stern gun when i go to mission.
I get the same thing - unless I go to the crew screen first, MOVE THE TWO CREWMEMBERS out of the gun position into the repair crew position. When the stern gun crew position is occupied you'll get that problem, if it's empty THEN you can replace with a bow cannon and it will stay that way.
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