Board Thread:Questions and Answers/@comment-88.0.101.31-20160810215834/@comment-27384850-20160812021726

It looks as though he is comforting her, though I don't recall the reason given in the web novel (if it's even the same as what it is here). He does the same for both Suguha and Sinon in their respective arcs, so it's not like it's something completely unheard of.