I host many of my smaller sites on a rented VPS. Occasionally - it's happened at least 4 times I know of - files on the server disappear. There's no rhyme or reason to it; one time it was a subdomain alias file and all my email stopped working, just recently it was an .htaccess file which caused a whole site to go fubar, the scripts weren't parsed by PHP, my source code got indexed; now my valuable source code is "out there" and my formerly solid #1 Google ranking has tanked.
Understandably, I'm furious. I used some rather impolite language with my hosting provider's customer service staff.
My hosting provider has no idea how or why it happened. They say maybe CPANEL did something bad. Other than that, they haven't a clue nor an inkling.
Has this ever happened to you?