We have altered the logic for how hashes.json is formed. Basically, before it was only giving the hashes for the original version. If there were any extra builds or patches on top, hashes.json was not updating correctly. So basically that list of files is close to the files that are different between the patch and the original unpatched version.
In addition to that, you were not receiving the file health checks for any files that last changed in a previous version, if you only opted to download files changed since the version after that.
In addition to that, if you previously downloaded a ZIP, and then you redownloaded it, all hashes it did contain were invalid on the subsequent download (if you compare the two, you will see that many hashes are truncated). This was due to one of our database columns not being appropriately sized for XenForo 2 file hashes.
With these corrections, future downloads should now have a more correct hashes.json.