My addon is using the SDK-module simple-storage for saving user settings and a history for restoring saved highlights on web pages.
Many users experienced a loss of their saved data, but I can’t find out how this is possible.
My question: Is it possible that Firefox sets back the store.json file (located in the jetpack folder) to its default state after shutting down irregularly (i.e. crashing)?
I don’t think you should spend time solving a problem like this. Migrate to a WebExtension. That won’t have this particular problem because it uses different storage mechanisms.