I noticed a missing image today, which threw a 403. Called my host and they said the file was actually missing, which is what I'm seeing via FTP. It turns out that several months of wp-content/2009 folders are missing 70% of their files!
I typically only access my site via the WP interface and FTP, and the site is pretty well locked down security-wise. The host is telling me that the last modification of that directory was done on June 5 and that "this was not done through FTP or SSH, but was probably done through the PHP web interface."
I have backups but am trying to determine WTF happened. I have made no major changes to the site during this time period. Has anyone seen this sort of thing before? I'm wondering if I have a security/credentials issue (although that would be a bizarre thing to do if someone did get in), or if there could be a host issue that caused this or...?