I had this same problem and it has been driving me crazy. While I still don’t fully understand the cause of the bug I finally found a way to fix it.
First a note, I think this problem only happens when the zoom accessibility mode is enabled, though it occurs even when not zoomed in. And further, it might be related exclusively to full screen zoom.
I have a keyboard shortcut that turns full screen zoom on and off (⌘⌥8⌘-⌥-8 by default), configured in accessibility settings. Whenever a region of one of my displays becomes inaccessible, I just zoom in and right back out and the inaccessible regions are gone.
I hope this helps.
Ctrl+Scroll-up by default zooms in the screen and Ctrl+Scroll-down zooms uit. Shortly zooming in and out using this way also fixes this issue.