I recently ran into an issue whereby when I created an item under a cloned node, none of the destination clones would pick it up.  Changes to the fields on the clone were working just fine.  Just no children would ever get created. I even had “ItemCloning.ForceUpdate” set to true, so it would automatically bring down the clones without approval being needed.

After a bit of trial an error, I finally tried to rebuild the links database.  It turns out the link was somehow borked.  After the rebuild, everything worked as it should!

To Rebuild the Links Database, open up the Broken Links Report from the Sitecore Desktop.

Click the “Rebuild links database” at the top of the screen and check the appropriate db.  (Mine was Master)

Now you should in business.