I FINALLY found out why NP++ as not saving my files properly. There’s a newish “Session snapshot & periodic backup” feature that saves a backup copy of all of your open but unchanged files, and any file changes. It also saves the current state when you exit NPP so if you close without saving, all of that is back.

However, it does not work properly. Once the backup interval passes, no further snapshots are saved, so whatever you had when you first created the file is all that will be saved. But, since the dirty flag is cleared, you cannot save the file normally either. Ctrl-S does nothing, silently. Closing a file does not warn you of unsaved changes. Closing NP++ does not warn you of unsaved files. You re-open, and it is back to what it was.

The way around this was to copy the contents, close the file, re-open the file then paste the contents, THEN save. OR, you could save as a new file.

But now that I know it’s this newish feature, I turned it off, and everything works properly.

Thanks to AdiranHHH from here:
http://stackoverflow.com/questions/24447786/notepad-doesnt-save-document-on-exit
And this open bug:
https://github.com/notepad-plus-plus/notepad-plus-plus/issues/337