I’m not familiar with Ctera - can you not roll back a specific folder?
“.hype” documents are actually a folder - the Finder just shows them as an individual file.
Pages and Keynote used to store files this way, but now their default is a flat file. (You can actually change back via the ‘File > Advanced > Change File Type’ menu). It would not surprise me if they did this to make sharing and sync services work better!