I once struggled with a variant of this problem: keeping local records of changes I made to a single source tree on a single remote machine.
I maintained a local copy of the entire source tree and a local svn repository to version the files. Instead of using netrw and looking for a way to save backups locally, I edited everything locally and needed a way to automatically propagate my changes to the remote machine.
solution 1: use a BufWritePost Autocommand to invoke scp to copy the file after it's been written. This can work efficiently enough if the system allows processes to share file descriptors, since it's possible to run a master ssh session to the remote machine and share the connection for subsequent sessions. If you are less fortunate (I was working on a windows machine at the time), the time it takes to negotiate a new connection for each file can be painful
solution 2: for windows, use WinSCP, which has a "keep remote machine updated" mode, in which it monitors a directory and all its subdirectories for changes and then automatically propagates the changes, given a set of rules (patterns to ignore, transfer mode for different filetypes, etc).