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How are you verifying that you're missing records? Are you trying to search the results of the union? Maybe you have partial results (screenshot below), in which case try adding a browse tool and then verifying if the records are there or not
There is a difference in the fieldnames? - take a look at the manually configure fields option in union and match your fields up. It might not be readily clear what the difference is in fieldnames but most likely that is the cause (name and name. or name and _name or name. vs name_ etc.) If that doesn't work - post some sample data because something in your dataflow may be skunky.
If you can post a screengrab of your union - after you have it as manually configure fields that also could help...
1. I think there is an issue with the Union Tool filtering option. When filtering to a specific item which we know is contained in one of the fields, it is not producing results. Is this a limit to size?
2. I had a Join Tool after which was fishing out the new records. Once that was updated, I had all records showing as desired.