Try to put the following line:

$mac2 = $2;
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before the substitution on $mac1.

I.e.:

if ($macs[1] =~ /(\S{17})\|(\S{17})/) {
                print "$macs[0] MAC1: $1\n";
                print "$macs[0] MAC2: $2\n";
                $mac1 = $1;
                $mac2 = $2;
                $mac1 =~ s/:/-/g;                
                $mac2 =~ s/:/-/g;  
                print "Converted Mac1: $mac1 Mac2: $mac2\n";
            }
[download]

The substitution:

$mac1 =~ s/:/-/g;
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which is a new regex, is basically clearing $2 and making it undefined.

update: fixed two missing characters while copying and pasting the original code to change it. Thanks to AnomalousMonk for pointing out.