Quote:
Originally Posted by Highbury
It's because you have probably submerged and resurfaced. The officer does not go back onto the bridge by default. Go to the crew management screen and put him back 
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Just another unsolved flaw in the game that no one has bothered or managed to fix. Its actually not that bad when you aren't using your WO all the time (like in a few fatigue mods where officers cant go 24 hours straight but burn out after 8 hours).