In addition to a possibility of the config files being stored in a temporary directory (unable to substantiate it without code), there is also the possibility that some code path in your code allows the configuration files to be removed by some invocation of your code.
I would do the following things (for starters):
- Check for any security advisories on your software, and apply fixes for those issues. This is extremely important for any public-facing server, not just web servers.
- check your configuration files and settings to ensure that you are not storing them in an area that gets periodically cleaned.
- Check to see that there are no external cleanup (or other) processes that can delete these files (see at, cron, windows scheduled tasks, and so on). I once saw a situation where important files on a shared filesystem were removed by a find process on another machine, because of a '-follow' flag and a symlink in a /tmp directory.
Additionally, you may want to get familiar with your code and learn how to (or contract with someone to) do a code audit on your system. There are monks around who make themselves available for consulting of this type.
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