The camera zooms in on the tearful Shinji; at the end of the cut he’s so overwhelmed he looks away.
SHINJI:“Don’t say sad things like 'Farewell' when you leave someone!"
(turns face away) "Uh…”
Xard: Looks like they decided to skip the zoom...
Kendrix: Rei never says "farewell" ever again, even if it almost was her catchphrase before. This shows us in retrospective how this occurence has impacted her - It is also an important point for Shinji, as he makes a visible positive influence on someone else's life. If he were to leave now, it wouldn't be as if nothing had happened.