Hmm...that sounds pretty weird. Uploading a file should not modify another file unless the two files are named exactly the same things which is not the case here.

I can not say for sure from what you have given me, if someone done this on purpose or if there is even a someone behind this. However if you are worry that your account has been compromised just change your password and hopefully that'll prevent future cases such as this.

What was in the index.php file?
We need to know what was in the file to know what it was for.

Some hosts set up the servers to place a default file in the public web directory.
This maybe the case.

It doesnt seem like it has been hacked, is there sensitive data being sent on your site (like transactions etc..) if not then it probably wasnt hacked. Look at visitor logs for a huge spike in traffic and bandwidth.