Yep classic SH3 bug.
I guess you had this officer in the Repair section of the U-Boat when you docked or finished the patrol. If you do this then anyone (sailors and officers) who is left in the repair section and not in a 'proper' U-Boat section (Torpedo, engine rooms etc) goes AWOL. The only way you have to bring him back is by loading an earlier save game before he was put on the repair section. Otherwise just release him via SH3Cmd and hire someone new from the baracks screen
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