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$append = 0;
if ($append)
...
{
open(MYOUTFILE, ">>clean_text"); #open for write, append
}

$append = 1;
...
...
{
    # Trample all over my irreplaceable data
}

my $append = 0;
my $cleanedFile = q{clean_text};
...
    open my $cleanedFH, q{>}, $cleanedFile
       or die qq{open: $cleanedFile for overwrite: $!\n};
}