I actually figured out a way to do it.
For some reason Hype had become corrupt and wasn't allowing saves, however I went into terminal and then opened a simultaneous instance of hype (two hypes running at once). You can do that by typing (making sure you include spaces).
open -n -a
Then a space and open quotes.
Now drag the hype application (from the application folder not the dock) to the terminal window, and a path to the app will appear, something like:-
(weirdly it says Hype2 on my machine, when in fact it's Hype 3).
Then close the quotes. The final text looks like this on mine:-
open -n -a "/Applications/Hype2.app"
Then press return
Once the new version opens I was hoping to copy and paste the Scenes across, but it seemed to load the document in the new app straight away. From there It saved first time