Welcome to the OptoForums! The best way to make sure the strategy you're working on it's what's in the controller is by uploading the archive in the controller -- assuming you have it down there. See this post about archiving (and making sense of a pre-existing strategy).
The process of upgrading WILL flag it as different. In fact, one of the features we added since 8.2 is a Checksum which helps you tell if you have a match between what you're downloading vs. what's down there. For example, here's what I saw when I created an 8.2 strategy, downloaded, opened it in 9.4, and when to download the converted-to-9.4 strategy:
Hope that helps!