You mean if it crashed A) while airborne inside FSDT area or B) even parked at the gate on ground inside FSDT area ?
Doesn't matter if it's inside or outside an FSDT area when it crashes. Regardless where it has crashed, it will not be able to save anything in the FSX.CFG that changed while in flight (regardless if you made the change manually, or the Addon Manager did because you were inside an FSDT area)
But in this case, having made a batch file to restore your preference would help with crashing.
In fact, maybe you *think* to have been forced to make a batch file to "defend" against the Addon Manager modifications (which as I've said, are not made if you fly outside an FSDT area and your previous settings WILL be restored when you exit from it), but the real cause was that, due to that particular add-on aircraft that always cause FSX crashing on exit, you couldn't set the ground shadows from the menu and keep the setting permanent, even if you never flew over an FSDT area to begin with.
So yes, in that case, the batch file might help.