Multi-site main site contents of image folders disappear periodically.

I have a weird problem I’ve never encountered before. Periodically, I havent been able to figure out when this happens, but the images on the main site disappear. When I go to the folders on the server, the folders are there, but they are empty. I reupload them, and all is back to normal, but this is getting annoying and my client is not happy either.

I checked with the hosting company and they said there is nothing they see on the server nor in the log files that would cause this. They also checke the chron jobs and there are none. They checked for viruses and there are none. This only happens to the main site on this multiSite installation.

Anyone ever heard of this? How do I fix?