http://bugs.winehq.org/show_bug.cgi?id=10142
--- Comment #18 from Eric Mullins emwine@earthlink.net 2008-07-15 02:03:37 --- Playing around with CMDOW, I was able to make windows disappear (from non-active desktops) using /NOT (making them not topmost), or /SIZ [W] [H].
I don't have the source for CMDOW, but both of those functions must be using SetWindowPos(). I couldn't get windows to disappear by simple activating/deactivating, however. The '/NOT' is interesting since it shouldn't have any effect, according to MS docs, for non-topmost windows.