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.

Apple's Official answer would be to reinstall your system since accession system files from Time Machine can be risky and tricky.

1. The system might be missing a file needed to assist in the recovery process and undefined / unpredictable results need more of an expert at the helm than using Time Machine to restore a photo or an app.
2. System files can be hidden and you'll need to know how to navigate to those folders by command shortcut as you restore the files from your Time Machine backup.
3. System files can have special permissions so you may need to fix them after restoring.
4. You may need to reboot after restoring and if you restore improperly, the system may fail to boot again.
5. Restoring from an old backup could undo patches or security updates and make your system harder to update. Having a recent backup can eliminate this potential problem.

Now ha the risks are on the table, here is how to proceed. 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.

Presuming you've done backups with Time Machine…

You can connect your TM disk, then while having your Finder window open to the directory the file was in, from 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 it back into your current setup.

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.