This happened to me too! Well, I didn't do it myself, but one of my co-workers overwrote the entire front page of our Canadian Web site in this exact way. She didn't even realize she'd done it! And I was getting frantic calls from Canada, "Why is my home page gone???" We were able to recover from backups but it was a tense few hours.
Be careful when uploading file names that are common among your directories, like "index.html". Overwriting is a pain, as "CC" found out:
It's a largish web site, with many many index pages, most of them in sub-directories. New employee edited one of the index pages and accidentally put it in the wrong level of the directory, replacing the site's home page. And then copied it to the same spot on the backup server. Our last local backup was two weeks old and we'd edited our complicated home page since then (we did have two copies so I'd thought we were covered). Thank heavens for google cache! Searched for the page, got Google's cached copy, viewed and saved the source code, did a little clean up and got it back online again. Whew.