This code has a well-hidden bug (or maybe I'm too tired): you always increment $i even if the equalty doesn't stand. Change

next unless $. == $array[$i++];
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to

next unless $. == $array[$i];
$i++;
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and it should work.

Also, you should really add or die "open: $! to your open statement.

Update: and to eliminate a warning, you may want to replace

next unless $. == $array[$i++];
print OUT $_;
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to

next unless $. == $array[$i];
print $_;
++$i < @array or last;
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