PRINT THIS PAGE, since you’ll be quitting Safari to do this, and the page will go away, eh?  🙂  I suggest reading thru all this before getting started…

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Here’s the problem: your Safari bookmarks are all messed up.

In my case, repeated syncings (and probably stupidity on my part) ended up with 10,700 bookmarks, 75-80% of which were duplicates. Not an ideal situation.

So, I used third-party software to remove the duplicates. I chose BookmarksDuplicatesCleaner from the app store, but what you use is up to you.

What needed to happen, after the bookmarks were fixed was to

1) make sure they didn’t automatically sync with iCloud right away, and thus end up with same mess all over again.

2) the iCloud bookmarks needed to be removed, and replaced with the new, clean list of bookmarks;

3) my other computers and iOS devices needed to get that new “master” list from iCloud.

There is nothing preventing Apple from making this simple to do… but they didn’t, so here’s the bunch of steps that I had to take to get it all done correctly.

The big picture is three stages: One – fix the bookmarks on my main Mac (easy – depending on the software you use), two – then replace the iCloud copy with that fixed list (too complex) and three – get all of that back on to all my other devices (simple).

stage one takes:

however many steps you want to devote to cleaning up your bookmarks. For me, it was two steps:1) buy and run BookmarksDuplicatesCleaner2) export the repaired list to an HTML file on my desktop 

Stage two takes 4 steps:

A)  —– (delete your old bookmarks)

B)  —– (delete the automatic bookmarks created by Apple) 

C)  —– (import your new, good bookmarks from stage one)

D)  —– (upload those new bookmarks to iCloud)

stage three takes one stepE)  —– (update your other devices)

stage one (get your Safari bookmarks fixed):

(I’m assuming that your main Mac is where all the corrective work is being done, and when it’s finished, your other devices will sync to the fixed bookmarks uploaded to iCloud by your main mac.)

First, run Safari on your main Mac and export (File/Export Bookmarks…) your current bookmarks to an HTML, just as a safety backup. (If something goes horribly wrong, you can just import this file and start over.)

Next, quit Safari.

Run BookmarksDuplicatesCleaner or whatever software you are going to use to clean up your bookmarks to delete the dups & do whatever other organizing you want.

Run Safari and see how the repairs look to you, and if it’s all OK, then export the (new) Safari bookmarks to another (different) HTML file. We will import that file later on in Stage two, so you MUST do this export!

(Now you have two files: your old messy bookmarks and your new cleaned bookmarks.)

stage two:

[Notes:  “Turn -OFF- sync” or “turn ON sync” as seen below, means you should visit your system preferences/icloud, (on iOS, this is in Settings/iCloud) and turn -OFF- or ON the sync button next to the Safari item.]

Stage two involves turning sync ON and -OFF- several times, and running and quitting Safari several times as well. Do not skip any step!

First, we are going to get rid of all your old bookmarks on all your devices and Mac.

(WARNING!!! You DID export those bookmarks in stage one, right? If you didn’t, you’re going to be very sorry if you do not STOP and export your good bookmarks now!)

OK: here we go…

On your main mac and on all other macs or iOS devices you have sync’d thru iCloud:

A)  —– (delete your old bookmarks)
1- Quit Safari.
2- Turn -OFF- sync.  
3- On your main Mac only, go to your ~/Library/Safari folder and drag the Bookmarks.plist file to the trash.  (If you see it being re-created automatically, it means that you haven’t turned -OFF- bookmarks syncing or that Safari is running.)
4- Run Safari, and if you see any bookmarks, delete them. 
5- Quit Safari.
[  Do this A) step for all your devices and computers before proceeding to B)  ]

B)  —– (delete the automatic bookmarks created by Apple) 
Now, JUST on your main Mac (NOT ON your other Mac or iOS devices!) :
Turn ON sync. 
Open Safari, and you’ll see that Apple has furnished you with a set of generic bookmarks. Delete them all.   Wait a few minutes to give iCloud time to delete the cloud version of those generic bookmarks. While waiting, your deleted Safari bookmarks should not reappear. You should have no bookmarks at all showing in Safari at this point
Quit Safari.
Turn -OFF- sync.

C)  —– (import your new, good bookmarks)
Run Safari again. You should see no bookmarks at all. (If you do see bookmarks, stop and check that you followed the steps exactly, until you can reach this point and see no bookmarks in Safari. Then proceed.)
Go the the Safari File menu and import the GOOD bookmarks file you exported (as the last step of stage one.)
(It may be necessary to quit and restart Safari to see your imported bookmarks.)
Using “Edit Bookmarks” in the Safari Bookmarks menu, make whatever adjustments and arrangements you want.
Once you have them as you like, quit Safari.

D)  —– (upload those new bookmarks to iCloud)
Turn ON sync. 
Run Safari, give it some time to sync, then quit and restart Safari, and make sure everything looks correct.
(If not, start at stage two all over again.)
At last!   Now at this point, iCloud should have a copy of your good new bookmarks.

stage three:

E)  —– (update your other devices)
NOW you can now turn ON sync on your other Macs and iOS devices. Everything should update correctly in short order.

Done  🙂  

(Remember: if anything goes wrong you can always restore your old, messed-up bookmarks, or your shiny new fixed ones, from the two exports you did in stage one. I assume NO responsibility for how these steps work out for you. I can only say that they worked for me.)