The strange thing is that I can re-import the ‘damaged’ images again manually with out problem! All of my edits survive correctly.
What happened initially was that I had done fresh install of Kubuntu on my computer along with the latest darktable (at the time; 2.4.4 I think). Since I had backed up my entire image library just before the OS update, after installing the OS, I simply opened up darktable and proceeded to import all of my photos.
Once the import was complete (it took a long time since I didn’t have OpenGL setup) I ran diffs between my xmp files and their backups. That’s when I discovered a large number of changes had been made.
I’m certain that I did not run any other photo application that might have messed up the xmp files.
At this point, I’m working on a script to identify the damaged files so I can re-import them again. I’ve re-imported about a dozen successfully so far, but I need to speed up the process.