Customer's domain is available in Hosted domains tab via CCPv1, but is not displayed in Domains section in CCPv2.
CCPv1 uses direct queries to DB to determine the content of page. In the meantime the CCPv2 uses APS to fetch domains owned by account. So, the most probable reason is corruption of APS resource of domain or the fact the it is linked with another account. This might be caused by issues in domain transfer, subscription transfer or with incorrect unprovisioning of old domain owner's account.
Contact Odin Technical Support.