I believe you are talking about CUCM publisher. Typically in the publisher is dedicated for admin activities and it is the subscriber who handles the call processing.
From what you mentioned, I understand you have a callmanager group with pub and sub. Is pub ahead of sub. The phones will always register to the highest available cucm in the group.
You might want to try re adding the cucm's in the correct order to the group and then do a reset of the phones.