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Hi djoseph, did you try my suggestion in post #7? It does seem to produce the desired output with the new samples..

Something like this?
awk 'NR==FNR{A[$2]=$1; next} $6 in A{$13=1; $14=A[$6]}1' FS=, OFS=, file2 file1
Otherwise post new samples..

You will find are many examples of this kind of join operation.. Try:
awk 'NR==FNR{A[$2]=$1; next} $12==1 && $1 in A{$6=A[$1]}1' FS=, OFS=, file2 file1

--edit--
Mornin' Don ;)