in reply to Perl - Remove duplicate based on substring and check on delimiters
Always, *always* check to ensure your file actually opened properly:
open my $fh1, ">>", "outputcontrol.txt" or die $!; open my $fh2, ">>", "outputoutput.txt" or die $!;
I don't know if that's the issue, but it's definitely the first thing to try.
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