There are quite a few issues with your script, if you put these two lines at the top you will get an idea:

use strict;
use warnings;
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See The strictures, according to Seuss for why.

To fix the most obvious try this (untested):

my %map = ();

while (<IN>) {
    chomp $_;
    my @items = split(/\,/, $_);
    $map{$items[0]} = $items[1]; # [1] not [2]
}
close IN;

my ($cur_awb,$cur_val);

while (<BASE>) {
    chomp $_;

    if ($_ =~ m/\<KEY_BOL_REF\>(\d*)\<\/KEY_BOL_REF\>/) {
        $cur_awb = $1;
        $cur_val = $map{$cur_awb}; # should do some error check here
        print OUT $_ . "\n";
    }
    # ... etc.
}
[download]