When I resume my computer from sleep, all WinSCP windows jumps to the virtual desktop (Windows 10) I'm currently using.
This is because the WinSCP automatically reconnects, and reconnecting activates a window which causes Windows 10 virtual desktops to behave weirdly when on different desktop.
Here is official MSDN docs about few public Virtual Desktop API's:
And here is a link to Russian forum with a unofficial APIs, which I can confirm works also:
Though I suspect you don't need to use any of these new APIs if it's enough to not activate the window when reconnecting.
Thanks, good work.