Incorrect sync setting on iCloud Drive: While setting up your iCloud Drive, you may have selected the option of keeping Desktop and Document files on the iCloud Drive. Common Reasons for Files Disappearing From Mac But before that, let's know why files disappear from Mac. You can either make some changes to your Mac settings, use Time Machine, or leverage a file recovery software to recover your lost files on macOS. If you're facing the issue of files not showing up on Mac SSD, hard drive, or external storage device, then don't panic. You may get startled when files present on your Desktop, Download folder, Macintosh HD, or Trash suddenly start disappearing. Recover Files through Mac Data Recovery Software.