I didn't read every single one of 10,000 plus lines but I did not see any duplicates of SEQN until the bottom of the file where apparently something other than data appears in the last 5 or 6 lines. So you need to describe what is keeping you from merging the file.
I'm not going to read the entire documentation on the NHANES website to determine what any of that data represents or the problems involved. I would recommend searching the site carefully as I doubt that you are the first person to attempt such and there is likely to be example code there. Just may take some digging.
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