use strict;
use warnings;

my $par_value = 3;

my $inData = <<INDATA;
wire [130 : 0] dgrs_1;
wire [130 : 0] dgrs_2;
wire [130 : 0] mgs_1;
wire [130 : 0] mgs_2;
wire [130 : 0] pqr_1;
wire [130 : 0] pqr_2;
int abc;
int pqr_1;
int pqr_2;
.dgrs_1(dgrs_1);
.dgrs_2(dgrs_2);
.mgs_1(mgs_1);
.mgs_2(mgs_2);
INDATA

open my $in_fh1, '<', \$inData;

while (my $line = <$in_fh1>) {
    if ($line =~ m{ \A (.*dgrs) }xms) {
        print "${1}_$_;\n" for 1 .. $par_value;
    }

    if ($line =~ m{ \A ("\.dgrs") }xms) {
        print "${1}_$_;\n" for 1 .. $par_value;
    }

    if ($line =~ m{ \A (.*mgs) }xms) {
        print "${1}_$_;\n" for 1 .. $par_value;
    }

    if ($line =~ m{ \A (.*pqr) }xms) {
        print "${1}_$_;\n" for 1 .. $par_value;
    } elsif ($line !~ m/(?:dgrs|mgs|pqr)/) {
        print $line;
    }
}
close $in_fh1;
[download]

seems sufficient to reproduce your problem. Check your regular expressions are matching what you expect them to.