Update: the baggage agent (not a red coat, but seemingly a supervisor) did a manual JFK-DCA-JFK-BOS on my bag. It followed me on each plane, but I didn't have to pick it up until BOS. I don't think it hurt that I'd been upgraded, too.

The agent said that she could manually put it in the system, and if it takes it would not be a problem. And, it wasn't.