1. The users would be reasonably happy with a silent one-click synchronization (a GUI version of the command-line /synchronize ... /defaults). No pop-up windows at all, just synchronize and refresh. They could then just hit Ctrl+S whenever they switched back to the Windows machine.
2. Even better would be a periodic synchronization, with WinSCP doing the silent synchronization every 60 seconds . This wouldn't involve directory change notifications, just running the ordinary synchronization each time.