Restarting unity messes up windows and kills other programs

[Andreas E.]

Sometimes unity silently disappears (still displayed on screen, but cannot be iinteracted with, and tty `pidof unity` finds no running process). When restarting unity with `unity --replace`, the following happens:

- all windows are moved to the wrong virtual desktop, which requires significant effort to get back to a productive setup

- several application windows (and the application processes) have become missing, usually the browser and Virtualbox (with the current work completely lost)

Expected behavior:
a) The window manager never crashes, or b) The window manager is restarted, all application windows are not negatively affected.

Ubuntu 16.10
unity 7.5.0+16.10.20161112-0ubuntu1