Hi @Dbell ,
The Storage Migration Service (SMS) will unfortunately perform a cut-over from the source to the destination server, so in your scenario it's unfortunately not a suitable solution.
You could simply use Robocopy / Xcopy to copy all the folders and files, with all the permissions, and then export -> import the registrt information which contains the information about the shares.
Saving and restoring existing Windows shares
https://support.microsoft.com/en-us/help/125996/saving-and-restoring-existing-windows-shares
Here's an example guide:
Migrate Files And Shares To Server 2012 Guide
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Best regards,
Leon