@voice-of-reason Digging up a slightly aged thread here (sorry), but wanted to comment on this too.
Some aircraft allow you to open a window in flight without the simulator causing the "overstressed" message, so I guess it's down to how the window is set up in the aircraft definitions.
With the Caravan and its state saving, I have found that when the aircraft loads up with the storm window already open, the simulator thinks it's closed and I can take off with it open. The engine sound remains quiet, as if the window is closed. If I click on the window, it visually closes but the sound volume remains unchanged. At this point it's "in sync" again. So if I click to open the window, it visually opens and the sound volumes increases (if on the ground) or the flight ends (if airborne with stress damage enabled).
I can (and have) turned off the stress damage setting now, but it would be nice if the above could go on a potential list for future fixes or optimisations.