Theme Files being removed

Over the last week, I have noticed that in my IFeature theme, the style.css was removed or not being recognized in my theme and then when I went to the site today, the entire themes files were gone! Does anyone know what may be causing this? Good thing I had a backup in place and could save some of what I was working on. The odd thing is when I look at my backups, its not showing the ifeature theme without any files being saved…and I have worked on the site and this theme days after it was backed up so it was obviously still there but didn’t get backed up…any ideas?