Oh, this is a different problem then.  iCloud Safari is a transaction-based syncing system.  Adding a bookmark, for example, is a transaction.  If a transaction is missed, the only way to fix it is to reconcile, but iCloud does not provide any way convenient way to do this.  Here is what you must do to get back in sync:

•  Make sure you've deactivated any utilities other than Smarky that might mess with your Safari bookmarks, such as Xmarks or old versions of Bookdog.  You should only be syncing with one of our apps: Smarky, Synkmark or BookMacster.

•  Enter Smarky.
•  Click the Syncing button in the toolbar to pause syncing.  It will indicate a red exclamation point, !
•  Switch on all of your devices that are syncing with iCloud Safari – your Mac(s), iPhone and iPad.
•  Launch Safari on all devices.

In the next section, you're going to delete all of your bookmarks.  This is easiest to do on your Mac.

•  Enter Safari.
•  Click in the menu: Bookmarks > Edit Bookmarks.
•  Select all items except the Favorites Bar itself and hit delete. Repeat as needed until you have only an empty Favorites Bar.

• Wait at least 30 minutes, or overnight.  Leave all devices on, running Safari.
• Check your bookmarks in Safari on all devices and delete any that reappear.
• Quit and relaunch Safari on all devices.
• Repeat the wait, check and delete until all bookmarks and folders are gone for good.

•  On your Mac, enter Smarky.
•  Click the Syncing button in the toolbar to resume syncing.  It will indicate a green dot and prompt you to export.
•  Export as prompted.

After another 30 minutes, all devices should have all bookmarks.

Although this issue was quite common when iCloud was new in 2011, iCloud has been getting better, and with luck you won't have to do this again.

Hello, Eric.

The fact that changes are making it to your iPad confirms that iCloud is getting them from Smarky.  And iCloud is apparently pushing the changes to your iPad, but not to your iPhone.  I had this problem on an iOS device a few months ago.  I was able to "fix" it by quitting Safari on the errant iOS device.  When I re-launched Safari, all of the new bookmarks which I had created on my Mac during the last two days suddenly appeared.

Of course, that's not the way iCloud is supposed to work.  New bookmarks should appear within a few minutes, without re-launching Safari.  So I filed a bug with Apple, but when they replied a few weeks later, I was unable to reproduce the problem.   The last time I checked, changes appear on this iOS device without re-launching.

Please try relaunching Safari on your iPhone and see if past changes appear.  If that works, test whether or not additional changes now appear without relaunching Safari.  To be sure, allow, oh, 30 minutes.

And please tell us the results.  I shall at least ding Apple again on that bug if you confirm the same problem.