In my experience it is better not to make any changes to reservations online, even if the system allows it. I've had this issue twice now, both times a call to customer service resolved it.
First time, I added my C&A number, and even though the price didn't change, the onboard credit disappeared. Second time I updated my phone number, and that caused price of cruise to go from $2000 to $3400 beause somehow it removed all discounts.