One of my relatives had a similar thing happen a few years ago, though not at GoDaddy.

In this particular case, they had "shared hosting" and it turned out the permissions on their particular directory were somehow left writeable by "other". In the *nix filesystem sense.

eg any other customer/user/etc on the server was able to overwrite the files. Which someone had done at some point.

Was easy to fix at the time (eg fix the permissions), but I have no idea if it occurred again over time.