it sounds to be an Operating system issue. Try to upgrade it.
Yes, definitely the OS. Mojave still does it.
One thing I haven't 'deliberately' tried is maybe hide apps before sleeping, that might keep the panel positions in place, maybe.
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Try turning on Window > Application Frame. That works for me. I have it on all the time. Same setup as you.
EDIT: I don't have a second monitor, but I've heard it works better with Application Frame on when two monitors.
thanks for your answers. There’s one new thing I found out: I usually switch off my external screens during sleep mode to save energy. When I keep them switched on during sleep mode, the panels stay where they are. But when I switch them off after going to sleep mode the system somehow moves all open windows to main screen. That’s kind of annoying as I have to reset my workspace every time I wake my Mac up from sleep mode. My Windows PC memorizes all window position even during sleep mode and with switched off screens. I would really appreciate this behavior on Mac.
Do you switch off your screens during sleep mode?