How do I resolve 'This number is registered to your Apple Account but not associated with this phone' after SIM change on iPhone SE?

I recently switched my son’s iPhone SE2 to a new network(Three). I put the new SIM from the new network into the phone to activate it before starting the phone number porting process (as per the network’s instructions), then put the old SIM back into the phone until its phone number was ported over.

Now that the number has been ported over, the new SIM is in the phone and working fine, but I get the following message in the setup for Messages and FaceTime:

”This number is registered to your Apple Account but is not associated with this phone, You can keep using the number for Message and FaceTime until it expires”

However, the number in question *is* his phone number i.e., his original phone number that has now ported over to Three.

Does anyone know what’s going on here and how I can resolve this e.g., have my Apple account recognise that the phone number *is* associated with the phone?

[Re-Titled by Moderator]