What do you mean by refreshing?
The .hype file is a folder with a .plist file (text) and resources (images, videos, fonts, etc). Windows machines will see it as a folder, but Macs should understand it as an openable file. It would be great to know at what point you start to see the package corrupted. By package, I just mean a folder-understood-as-openable-package in Mac OS terminology.
If you open & edit a Hype document tracked in a version control system, scene thumbnails will be regenerated within the package, the data.plist file containing the animation + element data will change, and any resource updates will count as changes. If you move elements around, adjust timing, and make adjustments to your document the key thing you want to commit is the updates you make to the 'data.plist' file stored within the filename.hype 'folder' and of course any resource additions / adjustments.
I don't have a lot of experience with SVN/Mercurial but so far Git for me has behaved as expected when committing .hype files.