I'm guessing the results will vary depending on the specific agents involved. This doesn't involve an infant, but my wife and I just got back from a trip and for some reason the kiosk timed out on the final step for my wife (but not me). It wouldn't let her try again, so the agent at the "X" desk (at SEA) had her fill out the blue form and processed her manually. We decided to try using the GE customs line, told the agent there what happened and presented my wife's NEXUS card. He just said that it was fine since she had her card and let us through. As long as you can show you're in the program, I'm guessing they'd be fine with it.