If I understand right dd does the physical disk not the folder structure your networked drive is not a part of the physical disk so it won't backup the contents of that folder not sure how it all works try this site to see.
https://wiki.archlinux.org/index.php/Disk_Cloning
I don't know but I think you can unmount the drive some how from that folder but still have the drive seen by Linux need someone with a bit more linux knowledge
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