If your data is always going to have that number of fields, you can just work from the front and the back and comma-join all the bits in the middle.
perl -F, -lane'chomp;print join("|",@F[0..2], join(",",  @F[3..$#F-4]),@F[-3..-1])' A/NSRLFile.txt

In reply to Re: swapping PIPE for comma in CSV file by pseudomonas
in thread swapping PIPE for comma in CSV file by dwhite20899

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