Deji,
Changing the mailbox store on Unity will use the same procedure as the one meant for changing the partner Exchange; the following two accounts are the ones that determines which Exchange server is the partner Exchange server for UNTPR5 and for UNTPR6 and moving them to another Exchange mailbox store without having the proper permissions will break the system:
Unity Messaging System - UNTPR5
Unity Messaging System - UNTPR6
*** Make sure that you follow these steps on both Unity systems (UNTPR5 & UNTPR6).
First, please run the Permissions Wizard and make sure that the second mailstore is selected.
Then, move the accounts to the second Mailbox Store.
Last, Run the MSCW from the add remove programs and select the new Mailbox Store (This will stop Unity).
Please follow the steps on this link since they have additional details about this procedure:
http://www.cisco.com/en/US/docs/voice_ip_comm/unity/5x/upgrade/guide/ex/5xcuruge050.html#wp1157854
Hope it helps!