I have been tripped up by this issue -- nearly missed an international flight because I was not allowed to check in online with a new passport. This was before they had the "take a photo of your passport" option on the app.
The system may not be able to accept a new passport number as "trusted" until an agent physically swipes the document or it is seen "in person" via the app.
I would suggest simply telling the system that you are on your old passport (if the date is still valid), and then at the airport, updating the passport details at the kiosk or with an agent.
It is probably not worth trying to fix this in advance. Far more trouble.
Last edited by TA; Dec 15, 2015 at 6:39 pm