A FREE Safari Bookmark Sorting App
When enabled iCloud syncing keeps all your Apple applications up to date with recent changes so you have the updates on all your computers and iOS devices. This wonderful cloud syncing is great when it works. Apple unfortunately has had a long standing issue with iCloud syncing and its various capabilities (remember Mobile Me?).
iCloud Bookmark syncing runs continuously in your systems background. It looks for changes and additions and then sends them to iCloud for storage. When you make an unusual amount of changes to your bookmarks iCloud thinks there has been an error so it reverts to a previously stored cloud bookmark listing. If you have multiple computers or iOS devices utilizing iCloud Safari/Bookmark syncing this is further complicated as mass changes are compared to your other devices and the cloud stored bookmarks.
Simply stated Apple assumes an error has occurred so it fixes your bookmarks automatically by reverting to a cloud stored listing.
If possible, gather all your Mac Computers and iOS Devices in one location.
Turn OFF iCloud Safari Syncing on master Mac computer
Run SafariSort to organize your bookmarks on you master Mac computer
Grab your iPhone/iPad (iOS device) and MANUALLY delete ALL your bookmarks and Favorites. You will only do this on ONE of your iOS devices.
Note: You will have to manually delete bookmarks in your Favorites folder via the above mentioned steps.
Turn ON iCloud Safari Syncing on master Mac computer
Hopefully you are now in Bookmark Nirvana.
From any Finder window select "Go" via the Apple Menu. With "Go" selected press the "option" key on your keyboard. A new option "Library" will appear in the Go menu. Select "Library".
From the Library folder locate and open the folder called "Safari". Inside the Safari folder you will see several files. The backup files are named "Bookmarks.plist_xxxxxxxx-xxxxxx" (Example: Bookmarks.plist_20160731-131537).
Delete the file named "Bookmarks.plist".
Rename your latest backup file to "Bookmarks.plist".
Open Safari and choose File > Import Bookmarks. Choose the Bookmarks.html file you previously exported.
Restoring Bookmarks from iCloud You can restore bookmarks via the iCloud website. Log into https://www.icloud.com and select "Settings". Scroll to the bottom of the page and select "Restore Bookmarks" under Advanced.