Thank you both.
I should have mentioned that it's a pretty old site and has been working for nearly 10 years.
Config not in a temp directory.
Possibility of a new vulnerability? I guess but it's no longer supported.
No files get deleted. They are where they always have been.

It has a setup interface accessed by deleting the location.pl file.
To restart I merely delete the timestamps and recreate the location.pl.
It's not the location file that's the problem as it times out while looking in the correct folder for a file that is there and does have the correct permissions.

Timestamps are the only files that get renewed.
To be honest, the entire site is being retired in a couple of weeks but it bugs me if I don't have logical explanations for things.

I was sure it was at the server end (ref two different sites having the same problem) but a new vulnerability is a real possibility. Thank You Both!!!