I'm not sure about a best long-term fix, but if you just want to regain control over an existing window, I found a good tip here (assumes you are running the "Mate" window manager with multiple displays).
The basic idea is that this problem seems to be some interaction with the "panels" and you can make the window behave by placing a panel on any edge of the second display. There are a couple of ways to do this, but the simplest to explain is:
- right click an existing panel on the other display
- select "New Panel"
- repeat steps 1-2 until a panel is added to the display in question
- use F11 to un-fullscreen your window
- delete any unwanted panels (right click, "Delete This Panel")
I have encountered this issue several times over the years (with widely different versions of Chromium). There are numerous hits on internet searches, and most of the solutions come down to various different methods "deleting the configuration". An unstated assumption seems to be that you will also find some brute-force means of killing the offending window, and that resetting the configuration will prevent this issue from occurring for new windows. Another, assumption must be that you don't mind losing your configuration data (such as bookmarks).