Are you saving on your NAS or locally?
Have you experienced this issue with any other tools on your NAS? The issue is that the AFP protocol is not great--Hype saves out a plist file during edits, and all images are saved within a folder within a Apple-based folder package. At some point the save might not have stuck. When saving (or autosaving), a temporary folder is created in the folder containing the .hype file and changes are written there prior to being applied to the original file.
(above: saving a file on a NAS)
I've seen this issue on Google Drive, on iCloud Drive (thought not as much recently), and network attached storage. Unfortunately this seems to be a network-related bug with how files are written to quasi-local storage. Turning of autosaving might reduce the amount of writes, but I don't have a fix unfortunately.