Blame it on iCloud! Seriously- blame it on iCloud. There have been many many many reports of bookmark madness occurring after users have edited, rearranged and/or deleted bookmarks from Safari. The following directions should help you get your bookmarks back in order.
Warning! Please follow the directions below closely and make a backup before you start. Note: This occasionally takes more than one try and it takes at least an hour to complete.
- Pick your Mac that has the best set of bookmarks.
- Copy your bookmarks file to a safe location (i.e. the Desktop). Launch Terminal via the Applications > Utilities folder. Copy and paste the following command in Terminal:
cp ~/Library/Safari/Bookmarks.plist ~/Desktop/
and press return. Verify that “Bookmarks.plist” was copied to your desktop.
- Turn off bookmark sharing on EVERY iOS device. Go to “System > Settings > iCloud”. Toggle the Bookmarks options to Off. Choose “Delete from my device” when prompted.
- Delete ALL bookmarks from Safari on EVERY Mac system. Via Safari; select “Bookmarks > Show All Bookmarks”.
- Wait for 30 minutes. This time allows for your bookmarks to be cleared from the multiple iCloud servers.
- Turn off bookmark sharing for iCloud on EVERY Mac system. Go to “System Preferences > iCloud” and uncheck Bookmarks from the list.
- Via your Mac with the best set of bookmarks, reset your original bookmarks file via Terminal:
cp -f ~/Desktop/Bookmarks.plist ~/Library/Safari/
and press return.
- Open Safari and verify your bookmarks are there. Via Safari; select “Bookmarks > Show All Bookmarks”.
- Run the SafariSort app to sort your bookmarks. Clean up any duplicates and make any further changes as needed.
- Turn on bookmark sharing for iCloud. Go to “System Preferences > iCloud” and check Bookmarks from the list. Select Merge bookmarks with iCloud when prompted.
- Wait for 10 to 15 minutes. This time allows for your bookmarks to be updated on the multiple iCloud servers.
- Verify all your bookmarks still exist after your brief wait. If they are still there you can now reenable bookmark sharing on ALL your other Mac systems and iOS devices.
Hopefully this returns your bookmark sanity. From this point forward your bookmarks should sync properly. If you run into issues again you will need to repeat the process above.