When you open a non-Gimp file, for instance a PNG, and you want to update the source file, you need to "export" to PNG. And if you close the tab, Gimp warns you that your work isn't saved, because it hasn't been saved in its native xcf format. There is no way to know if the work has been saved to the original file. At least, that was the behavior at the time.
So I had opened a dozen of (versioned) PNG files, modified them, then overwritten the PNG files. On closing, Gimp warned me that none of the images was saved. I ignored the warning since I didn't want to track the changes in xcf files. It turned out one the files had not been "exported" to PNG.