I’ve asked around internally, here’s what I was able to find out:
The settings aren’t supposed to get deleted with plugin updates. However, weird things can happen, and there are several reasons why settings can get deleted. Those could be ranging from uninstalling the plugin to re-install it if the update, for whatever reason, fails, to some really weird edge cases. Presumably, there are also some edge cases where the update itself might fail, etc.
All in all, the data should, therefore, persist and data getting lost gets considered a bug (if you have “all available information”, please pass feel free to send it to us), but the reality is: While I’m sorry to say this, there are just too many reasons why data could get lost (many of which are outside our control) and it is, because of this, incredibly difficult to track these down (I mean, we all know the feeling of plugin users sending us emails about bugs where we have no idea how to reproduce them ).
All in all: If you have detailed explanations of reproducible cases where this happens, please feel free to pass this info along to us (it is, officially, “a bug”). Other than that, I can only recommend not to store critical data there (i.e.: we, unfortunately, can’t guarantee for that data to be persistent).
Even though that’s probably not the answer you were hoping for, I hope it still helps a bit