I've just added code which should make the configuration more secure: rather than just overwriting the old file, phex now renames it to phex.bk, creates the new file, then deletes the backup. This of course isn't yet well tested, but it should help.

If the cause of the configuration file going missing is something else, maybe more work should be done. But until you try this out or give me more information I won't worry about this any more. :-)