This is hard to follow. But I would suggest starting by selecting the records you want from table 2 (non-missing values for score) and de-duplicating it. Then would select the records you want from table 3 ( Score2 IN("Negative", "Positive", "Non-conclusive") ) and de-duplicating it.
Then you would have three files each with a unique value, and you can merge them together without worrying about duplicates. If you want the flags, you can make them at that point.
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