It sounds like you may be on an insecure shared server, and other users have the capability of accidentally or intentionally deleting files on other hosting accounts. I've used a server once where someone deleted all server-created files on all hosting accounts in one sweep, causing serious problems to all the users on that server.
I've advise asking the webhost about this. A good webhost should have measure against this - not freely providing shell access, and locking down and scripting language (such as PHP) on the server.
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