Migrating files from old fileserver to new?

I have a silly question and can't seem to get past it... Hate questions that start like that. I'm using a robocopy script to move files from an old fileserver to a new fileserver. The problem is the old fileserver is extremely unorganized with most of the shares in the root directory of the drive. so what's happening is the script will copy the contents of the directory but not the actual folder the directory came from thus losing any of the permission set on the original folder.
What is the best way to copy folders in the root directory of a drive to new server but maintain the original folder and it's permissions?
This question is probably not in the correct forum so apologies if this is totally in the wrong place.. 
This topic first appeared in the Spiceworks Community

.. I think, usage of an ext. HDD (you get'em up from 60$) with a usb/fw port is best.
the old usb porst were usb1.. so, tranfer will need sooooooome time ..
another option would be..
even the very first iMac in 1999 came with an Ethernet port.. so, if you're able to handle it , you could establish a small LocalAreaNetwork between old and new Mac with a cross-patched Ethernet cable .. in MacOsX that is a single-clicker.. but, honestly, I'm not familiar (anymore) with sys8, which is I guess on your ol' colorful friend..

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