On your Mac open System Preferences > iCloud. Deselect the box next to Bookmarks then reselect then restart your Mac.
On any iOS devices tap Settings > iCloud
Switch Bookmarks off then back on then reset the device(s).
Hold the On/Off Sleep/Wake button and the Home button down at the same time for at least ten seconds, until the Apple logo appears.
I wrote a blog post about how to remove duplicates and then reset iCloud.
I had the same issue with thousands of bookmarks getting duplicated. I tried tons of steps until I found a way that worked. I then re-created the problem to see if my method would work again and it did.
First, did the app eliminate the duplicates locally on your Mac first?
Yes, it seems like the name for the bookmarks syncing is changed such that it is now called "Safari" instead.
I wonder if iCloud's Safari syncing has somehow changed since the step-by-step guidelines didn't work for Eiffel... The problem is that it's really touch to troubleshoot iCloud but I will try and get back here.
A bookmark file has been recreated automatically despite I have unchecked Safari in iCloud preference's pane.
I am so fed up that I am ok to completely delete the bookmark file. But I can't succeed even in this situation.
I have tested BookMacster without any more success.
It reports an error saying the Apple's iCloud is currently syncing my bookmarks. But I repeat my Safari option is unchecked in iCloud pref pane!!!!
I just did as follows:
1. Quit Safari
2. Make a backup copy of my ~/Library/Safari/bookmarks.plist file
3. Uncheck the Safari box on my Mac's iCloud settings pane in System Preferences.
4. Deleted the ~/Library/Safari/bookmarks.plist
On my system the bookmarks file was NOT automatically created. Of course, when I launch Safari, a factory default bookmarks file will be created.
I notice that Apple has updated their Knowledge Base article about troubeshooting iCloud bookmarks on iOS devices, especially interesting that they instruct to reset Safari and give enough time for the syncing to occur.. I am thinking that the issue is with iCloud and iOS since you get the problem with duplicates once you turn it back on on your iPhone. I suspect the bookmarks data in iCloud have not been fullly erased, which is aboslutely necessary in order to remove duplicates (since the 'syncing' actually will merge rather than sync the first time).
It seems like the guidelines i posted way back don't work any more (other than that Safari Prairiefire does it's job). I hope we can figure this out so I can update the blog as well..
I am getting really mad,
Mac Preferences / iCloud / Safari is unchecked on the iMac.
Safari is not running
Mac Min is running on Snow Leopard so, I think, there is no Sync with it. (and Safari bookmark is completely different and not sync with anything)
Safari is unchecked on the iPhone
Safari is unchecked on the iPad
And the problem remains. Again, again and again a new empty bookmarks.plist is created automatically. I have sent 100 to the trash. And again a new one is created within 1 min.
Do you have an idea? I used MobileMe in the past.
Thanks for your help.