Hi Jenna,
Thank you for your query.
It sounds really bad that your files are being disappeared. But keep the following in mind….
Wordpress Download Manager doesn’t delete uploaded files. Files should be stored in /wp-content/uploads/download-manager-files/
directory unless you have deleted them manually or move your server. Please check your /wp-content/uploads/download-manager-files/
directory to be sure if your files actually have been deleted or it is a path issue.
If you want us to take a closer look please send temporary wp-admin and FTP info in private reply.
With regards / Salahuddin Ahmed