[Is that really so surprising...? Or is he just being a little too pushy about it? Ken doesn't exactly sound upset about it, but Shinji can't exactly stop that thought from bubbling to the surface. Still, he doesn't really want to back off completely from his point.]

Sorry, [he offers it with sincerity, though largely as a matter of politeness after what he thinks may have been a slight boundary overstep,] you just seemed like you were in pretty rough shape before, and I don't want you to think that it would be... bad for you to take a little time to yourself, if that makes sense.