I checked Whispersync toggling it back and forth just to be sure but there was no change.
I fixed it by deregistering the Kindle app on my iPhone6s and then logging back in. Deregistering deletes your entire library but logging back in again triggers it to re-populate your library from your Amazon Kindle account
iPhone app: More/Settings/Registration Update/Deregister this Kindle. Then just log back in using your email address