Not only will they cancel the rest of your itinerary, they'll not reinstate it and allow you to continue even on standby unless you can convince them that you really did fly the segment in question. And, if you're supposedly connecting at EWR, you'd have to convince them not only that CommutAir didn't properly lift the missing segment, but that you also have a good reason to not have your boarding pass for the segment that you "just got off" as well as why you're outside security at EWR and not already at your connecting gate.