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Files don't really work that way. It's also a big risk to overwrite your originals. A program bug wipes out your input and output both.

Corona688 has already said it: throw away your originals only after being 101% sure your results are what they are supposed to be.

Once you are indeed sure you want to replace your originals use...

OK, try this very crude approach, which may need serious polishing:awk -F, 'NR==FNR {Ar[$1]=Ar[$1](Ar[$1]?"|":"")$2;
if (!Rr[$1])Rr[$1]=$2; next}
{for (i in Ar) gsub...