Did you look here as suggested?
Originally Posted by ~Darkseeker~
Have you checked in your favorites folder (C:\Users\USERNAME\Favorites) to see if they are actually still there?
If you can see the favorites there, I suggest you make a backup copy of them, delete all from the favorites folder. Then in internet explorer, do a full settings reset:
Click the white gear, select "internet options"
Click Advanced tab, then "Reset..."
Check "Delete personal settings" then "Reset"
Restart internet explorer, then copy your favorites backup back in.
If that doesn't work, you might have to reinstall IE 11 as well.