She is halfway through the system (it has a lot of moons, and a big asteroid belt) when she goes to bed again.
In her "morning", she observes that he has finished the job, thanks him, and proceeds towards the next system.
There is more interstellar space between the last system and the next. They are not there yet when she goes to bed.
When she wakes up, he is still in the copilot's chair, crying into his hands.
"...What has distressed you?" she inquires softly.
"Nothing new," he says hoarsely, sniffling. "You can ignore me if you want. I'm just gonna - " and he gets up and stumbles to the living quarters, where he curls up in bed to cry some more.
And then she follows him. "Something has changed. Today you are crying. Yesterday you were not."
"If you would prefer not to speak to me that is also acceptable, but - I do not prefer that you be distressed."
"I've been distressed for days," he says, somewhat muffled by the pillow. "It's just coming out now."
"You have not previously observed me to make use of my ability to suppress my emotions," observes Isabella. "Is it that which is disturbing you?"