Rebook BEFORE you go to the airport station kiosk. If it's after your scheduled departure time (regardless of how late the train is), the QuikTrak kiosk may not be able to retrieve your reservation, and there is no agent at the station to dig it up for you. If you're close enough to the CBS station anyway, you can go in there and have the agent handle it.
Overall, it's good to get into the habit of booking for the train you plan to take, before your scheduled trip, because once eticketing launches system-wide, a lot of stuff people are used to doing and getting away with won't work anymore.
People are already having some issues on the Downeaster because they skip their train without rebooking, and the system cancels their reservation and the print-at-home boarding pass isn't valid on a different train (which is different from how some people might work out a deal with the conductor to board a train other than the one for which they are ticketed).
Bottom line: Book properly before you travel. If you're not going to travel on the original itinerary, change your booking before you would have traveled.