Under "Active Directory Synchronization" settings there is only one Exchange Information Store av (4266011)

When configuring the "Active Directory Synchronization" settings there is only one Exchange server and only one Information Store available for selection. The planned migration will however occur on multiple target Exchange servers, and have mailboxes placed in multiple different storage groups and information stores.

Is this a limitation of the product?

Will it be needed to move the mailboxes post migration using native Exchange tools?

When performing mailbox switching later and using CPUU  will the users be automatically re-rerouted to the correct mailbox?

When specifying this setting in QMM only one Information Store can be selected. This is by design and does not cause any inconvenience. Selected information store will be used to mail enable the objects only.  This information is needed to allow the Exchange Recipient Update Service to properly mailbox enable objects.  At no time, with the Directory Synchronization Agent ever create mailboxes within the information store specified. 

Later when configuring mailbox synchronization collections, the collections will be pointed to the appropriate information store on different target servers. This location will be where the actual mailbox will be created when the mail target agent logs onto it for the first time. 

Even if a mailbox was accidentally or intentionally created on one information store, the QMM agent has the ability to move the mailbox to the correct  information store.

This step does not affect CPUU . When mail synchronization is complete, and the mailbox is switched, then the mail source agent will place a hidden message for CPUU within the mailbox. This hidden message will contain the target server name.

Note: for a more detailed description of the EMW process, please review the CPUU documentation included in the product download.