Well, periodically he had o go to her to be filled full of fresh nanites after he died.
1, She didn't tell him how intimate and sexual the process was (for her.).
2. Quid pro quo. If she was filling him up, it's only fair that he returns the favour.
3. Possibly the colony of nanites inside him creates a limited collective between the two of them and their subconsciousnesses were inextricably linked coitally always.
4. Unimatrix negative one. They were boyfriend and girlfriend in their dreams and forgot about it when they woke up which curbed her urges to pounce on crewmen for gratification.