Did you send him to the "Repair" compartment when you got banged up? And leave him there when you ended the patrol? They can get lost that way.
Commander is supposed to find and restore missing officers - did you exit the game and reload it through Commander in between patrols, or just end one patrol and start the next without exiting the game and restarting it via Commander?
I had an officer go missing once - he was the 'extra' guy I'd taken on as an engineering trainee so I'm pretty sure I had assigned him to Repair right off and just left him there. My system crashed during my first session on that patrol so I ended up just going back and reloading the "in base" save from the start of it - when I did, and got into the game again and looked at crew managment, that officer was gone. I finished the patrol and after exiting the game entirely and opening Commander, he was back on my crew list.
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