Rebuilding iCloud Bookmarks

Q.  I have switched on iCloud bookmarks syncing on my Macs and/or iOS devices (iPhone, iPad, iPod Touch).  But changes that I make don’t “stick”.  New bookmarks don't always propagate to other devices, or after a few minutes, bookmarks that I've placed in folders get moved into the loose BOOKMARKS, deleted bookmarks reappear, duplicates appear, or new bookmarks get deleted.  How can I fix this?

Cause and Pathology of this Problem

We think that problems like this occur when iCloud does not have proper records of bookmarks or folders.  We’ve identified three possible causes of this…

• In rare cases, if sync messages passed over the internet between iCloud and one of your devices do not arrive repeatedly, and iCloud just can’t recover.

• If you have been managing Safari bookmarks with a bookmarks management, sorting or syncing app which has not been carefully engineered to work with iCloud as our products have been.   If the developer of an app cannot convince you that their app has been engineered for compatibility with iCloud, you should either stop using that app or stop using iCloud Safari syncing.  Compatibility with OS X 10.8, 10.9 or beyond does not necessarily mean compatibility with iCloud.

• If you have have restored your Safari bookmarks file (~/Library/Safari/Bookmarks.plist) from a Time Machine or other backup while iCloud Safari syncing was active, or if the restored file was last modified when iCloud syncing was active and the old iCloud data was not stripped out before restoring it  (Don’t do that any more.)

When iCloud gets a command from one of your devices (Mac or iOS) to update bookmarks in such a way that affects existing bookmarks or folders that it does not have a proper record for, it may silently ignore the command, or relocate or delete affected items, or neighboring items.  Also, because iCloud doesn't tell you when it takes one of these evasive actions, it may take weeks for you to realize that something is wrong, and all this time the bookmarks disorganization may be compounding.

Overview of Solution

Since it is not practical to figure out which bookmarks and folders are not recorded properly in iCloud, the only solution is to extract your bookmarks from iCloud, drain the swamp, make sure all of the poision is out, and then replace your bookmarks back nicely.  The instructions below assume that you’re going to use one of our bookmarks management apps (Smarky, Synkmark, Markster, or BookMacster) to extract and replace your bookmarks.  Our apps give you several three-day free trials.  Alternatively, you can modify the steps that use our apps - for example, you can export from Safari and then later import from the file you created during the export.

Know How to Switch iCloud Safari Syncing On/Off

Throughout the process, you'll be told to switch iCloud Safari syncing on or off.  In this section, we explain how to do that.

Mac OS X Computers

• Click in the menu:  ▸ System Preferences
• Click iCloud.

Screen Shot 2013-12-13 at 07.30.00

You will then switch the Safari (Bookmarks) checkbox on or off, as instructed.  When switching on, you will be presented with this ominous warning…

Screen Shot 2013-12-13 at 07.27.20

When presented with this, you must be brave and click Merge.

iOS Devices

Same idea, slightly different.  Activate the Settings app, then click iCloud from the left sidebar.  The Bookmarks or Safari control is a slide switch instead of a checkbox.

The Steps

Now that you what you're doing, it's time to roll.

• If practical, get all of your devices (Mac, iOS, and PCs running Safari for Windows) in the same room.

PART ONE: Stash the desired bookmarks

• If you have been using Smarky, Synkmark, or BookMacster, make sure that you have Paused or disabled Syncing in your Bookmarkshelf document on all of your Macs.  After doing so, verify by checking that the Master Off menu item is disabled and indicates zero Workers and zero Agents.  It should look like this…


• If you have not already done so, on a Mac, get all of your desired bookmarks into a BookMacster Bookmarkshelf document, or into Smarky, Synkmark or Markster.  How you do this depends on where are the desired bookmarks.

   • If Safari has the bookmarks you want, import from Safari by clicking in the main  menu: File ▸ Import from one
 ▸  Safari.  Read the instructions which  appear and, depending where are the bookmarks you want, consider
      whether  you want to do a Normal import, or combine bookmarks with an Overlay.

   • In case you have lost bookmarks recently which you want to recover, other methods are explained in
       Restoring Bookmarks of Yesterday.

• If you are using Smarky, Synkmark or Markster, activate its document window.  If you are using BookMacster, activate the window of the document you now have the desired bookmarks in.

The next two steps, making a backup for safety, are not necessary if all goes well, but recommended if your bookmarks are important to you.

• Hold down the command (⌘) key on your keyboard and click the title of the window, Whatever.bkmslf.  A Finder window will open, showing the .bkmslf file.

• Make a back up copy of that file.  Depending on how much they mean to you, you might want to copy it to another computer, to cloud storage or other offsite backup. 

• Back in the .bkmslf window again, click the Content tab, and the Name column heading.  The numbers in parentheses after the name state how many bookmarks and folders you have.  Note the approximate sum (bookmarks + folders) of these numbers for later.

PART TWO: Clean Out     

• On all of your devices (Macs and iOS, Windows PCs), switch off iCloud Safari syncing (as described above).  When doing this on an iOS device, it might ask you this…

Because you've already stashed your bookmarks, in Part One, and this step is to clean everything out, the correct answer is Delete from My i<Whatever>.

• Choose one of your devices on which to work, preferably a Mac, the one with the biggest screen you’ve got.

• On your chosen device, switch iCloud Safari syncing (back) on.

• Delete all bookmarks and folders in Safari on this device.

    - If the devices is a Mac, activate Safari and click in the menu: Bookmarks ▸ Edit Bookmarks or Show All Bookmarks.
      In the window which appears, delete all bookmarks and all folders.

    - If the device is an iOS device, activate Safari and click the "open book" icon near the top left.  Swipe each folder
      to the left (iOS 7) or right (earlier iOS) and click Delete.  

• Recall the number of bookmarks + folders that you had and divide the number by 100.  For example, if you had about 900 bookmarks and 100 folders, the total is 1000.  Divide this by 100.  The answer is 10.  Whatever answer you get, go off and do something else for that number of minutes, or longer.  Longer is better.

• After the wait, if any bookmarks have reappeared, delete them again, wait again (the length of the wait depends on how many bookmarks you deleted this time), and see if they reappear again.  

• Repeat the previous 3 steps on all of your Macs,  iOS devices and any Windows PCs running Safari.

• You should now have iCloud Safari syncing switched on, in all your devices, and no bookmarks or folders in any of them.  The hard part is over.  This is a good time to take a break.  Come back tomorrow, check all of your devices again and make sure that no pesky bookmarks have reappeared.

PART THREE: Restore to iCloud    

• Activate Smarky, Synkmark, Markster, or your BookMacster document.  Click the Content tab.

• Reorganize your bookmarks until all is like you want it to appear in Safari.  In particular, you may want to use the menu command Bookmarks ▸ Find Duplicates, or Bookmarkshelf ▸ Find Duplicates, and then delete duplicates.

• On your Mac, if you had paused or unconfigured syncing by Smarky, Synkmark or BookMacster, Resume or reconfigure syncing, performing an Export when prompted.  Otherwise, just Export by clicking in the menu: Bookmarkshelf ▸ Export (Safari), or if Safari is not configured as a permanent Client, or if you are using Markster, File ▸ Export to one Client ▸ Safari.  

This should push all of the bookmarks saved in Smarky, Synkmark, Markster or BookMacster out to Safari on your Mac, and after that is done, iCloud will push them to your other devices.  Each of these pushes may take several minutes or more.  The same calculation you did before (total number of items divided by 100) applies.

PART FOUR: Feel free to Complain

You may wish to submit feedback or a bug report to Apple, requesting that they provide a web interface to Safari data in, or at least a Reset button to Delete all my bookmarks and start over.