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Can you upload some screenshots or the packaged flow file so volunteers here on the Community can see what you're seeing? It is very difficult to say without seeing any of the data or the flow in Prep, but one possibility is that Prep by default shows a sample of the data. You can change this to show the full data, but I'm not sure if that is what is causing the confusion or not. If it is the cause, this may be helpful for you: Join or Union Data
Let us know -- and happy analyzing!