Thank you for your post.
I am not getting a crash of the Dock. Using FileMaker Pro 14.0.3 under Mac OS X 10.11.1, this is what I have done:
1. I created a database file, TEST.fmp12.
2. I made the window Full Screen by clicking the green fullscreen button in the upper left corner of the window.
3. I positioned my cursor near the top of the screen, and the FileMaker Pro menus appeared. I selected New Window.
4. With "TEST-2" now showing, I made that window also full screen.
5. Under Mission Control, I merged the two windows into split screen.
6. I selected "TEST" and "un-Full Screen" it.
7. I closed "TEST-2", and although I got a black screen, I was able to scroll down to the bottom of the screen, and the Dock appeared where I could select FileMaker Pro to show TEST.
Let me know what I am doing differently than you.