4TB MyCloud moving to PR4100 with two 12TB drives... best way to move all data?

Yes and no. WinSCP is basically just a GUI interface for an SSH client. It may still be up to the user to issue specific Linux commands to get the copy process to run in the background on the My Cloud so the user can then close the WinSCP application while the copy process continues on the My Cloud.

Really though just about any SSH client can be used to issue Linux cp or rsync commands to the My Cloud OS and then leave it to the OS to run the copy while the client application window is closed. Assuming of course WD didn’t remove things like nohup from the My Cloud OS. Its just a matter of issuing the right string of commands like nohup in addition to the cp or rsync commands. Later one can reconnect via SSH to check on the status of the cp or rsync process using jobs -l or top.