splice is a convenient way to remove things from the start of an array. For example, you could pass the start line as a parameter to your script and then use:

print "Skipping $count lines";
splice @lines, 0, $count;
...

my $current_line_number = $count;
foreach my $line (@lines) {
    print "Processing $current_line_number\n";
    ...
    $current_line_number++;
};
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