Had this problem for my son (got an emergency passport renewal, but could not update his GE account). Had to stop at the "interview on arrival" booth and they had not issue updating it. Actually, while there was a bit of a wait for interview on arrival, they efficiently processed three tasks for me (renewal interview for me, update one child's passport, and update second child's picture to see if we can dispense with the "X").
Was also told by LAX enrollment center, to use enrollment on arrival to make any changes as long as the registration is still valid or a renewal is paid for before expiry. They can also change passports if you have a renewal mid-process where you cannot change passport info.