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Do you have a taskbar? Did they disappear from there too?
I run KDE plasma desktop on my laptop, and my home and work monitors have different geometries.
On display attach/detach, the desktop moves windows around rather intelligently but sometimes the geometry messes up and the window may end up atbsome ridiculous coordinates outside display areas.
On a desktop computer with multi monitors, the displays are loaded one after another at boot or resume from display-off mode, so the same geometric bug can still trigger.
The missing programs were not on the taskbar, they just poofed away all at once as if they'd been closed. (Nothing on taskbar for other workspaces) Certainly didn't expect one to reappear a few days later. >.<
If it's some esoteric geometry bug, it's a darn tricky one.
Wow. I hear the X-Files theme.