Does anyone have any idea how can worpress auto delete files that are uploaded with FTP to wp-content/uploads? There are no errors in logs other that the file transfer was completed succesful. Can the sites .htaccess do this? I'm using config CGI, suEXEC and for php i have CGI, is this correct for wordpress sites?
CGI is really slow and should not be used anymore, better use php-fcgi or php-fpm. But that's most likely not related to your issue. You can try to turn php errors on to show on the screen temporarily, maybe there is a permission issue.
Whicht type of files are getting auto deleted? Regular files shouldn't be removed by WordPress. Are you using any security plugin? That could be the reason. Checl ftp logs as well
