To answer your question, it is necessary to know the cause of it.
One of the cause can be hacker attack. To find the exact cause, it is necessary to look logs of statistics of site on a server.
And it is even better to write a security script which will scan all entrance variables, and to search for dangerous fragments. Such scripts are ready for the some CMS, for example PHP-NUKE. Such scripts help to prevent attacks, and to find vulnerability.
If I will have free time, I shall write article how to make similar security scripts.
If your visitors have the right to load files, vulnerability can be here. Someone has loaded a file *.php which has removed all. As it is necessary to look all commands fopen, fread. Probably, someone has crack access to administration. It is simple, if you do not have protection against pick up of the password.
Necessary to view the logs of statistic of site on a server.