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iCloud Safari syncing just stopped worked about 3 weeks ago for one of my computers, and I cannot make it work again, I’ve clear and clear and re-synced each of my computers and iPhone. Finally, I just gave up and use Dropbox now.
Just move Library/Safari over to Dropbox somewhere, and create a symlink back over, presto is just works.
iCloud has been a travesty ever since Apple started this, I’m surprised they cannot give you simple management like Dropbox to see WTF is syncing what, and a simple way to delete and resync things like your book marks.