I have a similar issue also. It's infuriating.
My macbook is connected to an external 4k monitor, which is the main monitor.
If I switch to a full screen app and stay there a while, then go back to the desktop, all open windows will be off screen, in the far right. I have to go to mission control, drag the windows to away from the external monitor and to the macbook desktop, and then move them back again to the main monitor.
I hope they get a fix soon.