You didn't mention using the "Sync My Kindle" choice in the gear menu of your Kindles. That might help.
You can connect your devices to a PC and look at the last modified date for the book files in the "documents" folder. That should tell you which books were updated recently.
If you knew which books you updated you could tell if any that should have changed did not. Even without that information you can still check your devices against each other to see if the same books were updated recently on both.
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