Your best course of action to retain single instance storage, is to us the procedure to replace old hardware with new. This is outlined in TechNet article 155216, but I'll outline the steps below:
This must be done when you can have e-mail unavailable for about 4 hours.
Move the mailboxes back to the original server and remove the server from the site.
First, ensure you have a current backup of the existing server.
From Exchange Admin, open the properties window for the server. Select the Database Paths tab and note where each item is located.
Stop all Exchange services and set them to manual startup.
Ensure there is a local administrator account on the server.
Rename the server and restart.
Delete the original server name from the domain.
On the new hardware, uninstall Exchange server.
Once the original server's name has disappeared from the server manager window, rename the new server using the original server's name and join the domain.
Install Exchange server on the new hardware using the same Organization, Site, and Server names used on the original server. Ensure all NT and Exchange service packs have been applied that were installed on the old server.
Run Exchange Optimizer and make sure the database paths match the information gathered from the original server.
Once Optimizer completes, stop all Exchange services.
Find the following folders on all drives: mdbdata, mtadata, dsadata.
In each folder, create a folder named 'Hold', and move the contents of the folders into the respective 'Hold' folders.
COPY (DO NOT MOVE) the data from the above folders on the old server to the corresponding folders on the new server, being careful to move data from drive C: to drive C:, D: to D:, etc.
When all data has been copied over, open a DOS window and execute the following command:
c:\exchsrvr\bin\isinteg -patch
When this completes, you will receive a message that the database was successfully updated. If you get any errors, try changing the directory to the drive and folder containing the priv.edb and pub.edb, and try again.
Once you have received the message that the database was successfully updated, you can start the Exchange services. If you had installed the internet mail connector on the original server, you will have to re-install it on the new server.
Once the server is up and running, you can delete the 'Hold' folders.
Let me know if you have any questions.
Bob