I did try to go through the logs to identify the reason the files were cleared, but unfortunately I'm not seeing any major deletes or anything that would have explained it. I was able to see someone modifying FTP accounts on 7/28, but that was all. I will freely admit that for this type of issue I'm no expert at log searching (my searches generally are just done to confirm the actions a user claims weren't performed by them actually were, such as uploading phishing pages or warez) so I may be missing something, but I don't see anything that would confirm or deny if it was a compromised password.
One thing that could potentially have caused it however is if a script on the account was compromised, and was able to run arbitrary code. If files were deleted via PHP commands, it wouldn't show up in the logs. I will admit it'd be an unusual compromise in that it wasn't used for something else, like sending spam or running unauthorized shells with malicious intent, but it is one I've seen in the past with a different service provider. Again, not a guarantee, just a possibility.