Thanks Jon, I am going to try your suggestion. Our receptionists happened to look at a patient imported items and AC reported missing links. Then they found couples more. I ran AC utilities to repair missing links then they generated a 20 page list (only about 30+ folders, some completely empty, some with few left).
Quite a mystery as only 30+ out of 4000+ folders. I don't think Synctoy would delete them as what echo option does is only to sync from my main computer folders to backup folders. This little program is quite effective and free. AC has missing files repair link options means files missing are not that uncommon .