Apple's Official answer would be to restore the files from your Time Machine backup.
If you use Time Machine, connect to your backup disk, then open Finder window open to where the missing file was last seen. You may need to use Command-Shift-G to go to system folders - if so, just be prepared to use that shortcut once you enter Time Machine as it has a habit to show a user folder when it starts.
Use the Time Machine menu in the menu bar select Enter Time Machine. Navigate back to a date the file existed, select the file, then click Restore (lower right button).
It will copy the file or folder back into your running system. At this point, make a backup and consider rebooting to allow the system to notice that the missing files are now restored.
