So, one thing that’s not clear here. Is the server and your desktop both at the same location? If they are I see no reason why you couldn’t just leave all the files on the server, have an NFS or Samba share then just stop it on the server and start it (over the network share) on your desktop. It would be functionally seamless, would require no effort to keep the files in sync, and would ensure your running things in the box you want.
So, one thing that’s not clear here. Is the server and your desktop both at the same location? If they are I see no reason why you couldn’t just leave all the files on the server, have an NFS or Samba share then just stop it on the server and start it (over the network share) on your desktop. It would be functionally seamless, would require no effort to keep the files in sync, and would ensure your running things in the box you want.