1. Open ssh terminal to remote server
2. Begin scp transfer as usual
3. Background the scp process (Ctrl+Z, then bg)
4. Disown the backgrounded process (disown)
5. Terminate the session (exit) and the process will continue to run on the remote machine.

http://unix.stackexchange.com/questions/65116/does-a-scp-transfer-close-when-i-close-the-shell

http://unix.stackexchange.com/questions/89483/keeping-a-process-running-after-putty-or-terminal-has-been-closed

http://unix.stackexchange.com/questions/103731/run-a-command-without-making-me-wait

http://unix.stackexchange.com/questions/4004/how-can-i-close-a-terminal-without-killing-the-command-running-in-it