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
Best Answer
You need to reset your Safari Bookmark. See this:
How can I reset the Safari bookmarks in iCloud?
Simplified steps:
The original author of these suggestions noted the following: "Once I turned syncing back on each device remained blank for quite some time. I’m not sure why but I was able to prod the system along by adding a fake bookmark on another device. This seemed to kick everything into gear and I was able to delete that fake bookmark on different device – which eventually deleted it across all devices."