The issue has since been fixed by Microsoft, however the recovery for those affected is unfortunately not quite automatic.
If you've purchased the Hyper Pro features, and they are currently unavailable to you due to this bug, here's what you need to do to get them back:
- Close Hyper (make sure it is completely closed, not just minimized)
- Re-open Hyper
- Try using a Pro feature; You should see the prompt to purchase
- Click 'I want it'
- (The screen will dim for a little bit)
- The Pro features should be activated again; You will not be charged again for the features.