After CPUU is run read receipts are sent out to email originators that have already been sent previously.
When emails are sent to unswitched users with the read-receipt option selected & the message is migrated before the source message is read, its "unread" status is also migrated. If the un-switched user reads the message in source, a read receipt will be sent to the message originator as normal.
When the mailbox is finally switched & CPUU is run against it the read/unread status of messages in target is processed to match that in source. When a message is marked as "read" CPUU uses normal MAPI processes which cause a further read receipt to be sent to the message originator.
It is possible to prevent the tool updating read/unread status by using the "-Skip ReadStatus" switch. Details are in the "ClientProfileUpdatingUtility" user guide.
However this will result in the read/unread status in target not matching the status in source at time of switching.