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Joomla configuration.php file empty after making changes in Global Configuration

We ran into an interesting problem today with a site running Joomla 1.5. We update this site every day and as part of the process, we put it into offline mode until the changes are complete. As we have been doing this every weekday for over a year, we have become conditioned for it to work correctly. So it was a shock when suddenly the site broke with a less than helpful error message. Both the frontend and Administrator were inaccessible. We manage the server hosting this site and I had noticed some unusual activity in the log files which I check every morning. So I immediately suspected that the problem was somehow associated with this. As this is a priority website, I panicked and thought that the server had been hacked. I wasted time checking this and other settings. 

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