I am frustrated by this issue that just appeared recently.
No matter what I do, any modification (rearranging, deletion) to the bookmarks are soon reverted.
the bookmarks are now totally out of sync with my iOS devices.
OS X version 10.11.3 (15D21) Safari Version 9.0.3 (11601.4.4)
Pls see my youtube vid for demo of the issue: https://youtu.be/ktxo1VVEwBI