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the way we would do it is first create a duplicate of the destination via phpmyadmin (operations>copy table with data/structure) then write a simple php script to read the one you want to merge, and as you loop thru the results, import to the duplicate version passing only the variables that are required to make the entry valid in the copy. Once you confirm the data is correct, u can rename the tables via the same way (operations>rename) and make it live without any hiccups.
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