Debugger force some refresh of window or field, it could be cause.
Is there any export records or field contents step that would overwrite the file?
Turns out it was a very obscure thing happening. There was another database file contained in a container field, and this was being published to the same directory, overwriting the old one - except there was some error happening, so that it didn't actually replace the original file. In effect, it was just deleting a file. All set now.