As you mentioned you can use the Set-ClientAccessArray cmdlet to modify the FQDN of your CAS Array. You will need to make sure that the new FQDN points to the correct NLB Virtual IP address for your CAS Array configuration.
You would then configure your mailbox databases using the Set-MailboxDatabase -identity <databasename> -RpcClientAccessServer <CASarrayFQDN> cmdlet.
I would recommend that you make these changes after hours when most of your users are not connected to Exchange. Once the changes are made and the users connect with Outlook the client profile will be configured with the new CAS Array name in the Exchange Server field.