...
    chomp;
    $hash{$_}= $pbxex-1 if (not exists $hash{$_});
    $hash {$_} ++;
...
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This is one way, initizalize the hash with your base value whenever you want to increment a value that wasn't accessed yet. In this case the base value is one less than the starting value because there is an increment following the initialization

Another way would be to add 2 to every value in the hash after you read in all values from the file:

...
    chomp;
    $hash {$_} ++;
}

foreach (keys %hash) {
    $hash{$_}+= $pbxex-1;
    print PBXNUM1 "$_$hash{$_}\n";
}
[download]