I was wondering this earlier myself, so I did a quick tag search, and the only time they've encountered was in post #303287 at which point Neru was probably far too embarrassed to notice her. She has however heard of her from Miku before ( post #301137 ) but didn't make the connection.
In the badminton game, Rin called both Len and Miku to come back, but maybe she was standing from far of them so Neru didnt notice, or the sadness already engulfed her by then