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.