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|value 1|value two|"|Value 3 was "NULL"|2001/06/06|

perl -pi.bak -e "s/\|\"\|/\|\|/g" filename

open OUTFILE, ">>@ARGV[0].dat";
while (<>) {
...
    print OUTFILE $_;
}
close OUTFILE;

while (<>) {
    split /\|/;
...
    }
    print $output;
}