Thanks Guys! tr introduced difference almost 500%, I managed to clean up the binaries, below is the final code:

#!/usr/bin/env perl
use warnings;
use strict;
use Text::CSV_XS; # also install Text::CSV_XS for speed

my $csv = Text::CSV_XS->new({ binary=>1, auto_diag=>2, escape_char=>'\
+\',
    eol=>$/, quote_char=>'"', sep_char=>";", always_quote=>1 });
while ( my $row = $csv->getline(*ARGV) ) {
    $row->[5] = pack 'H*',$row->[5]=~ tr/://dr;
    $row->[5] =~ s/\A\x19\x68\x09\x24\x00+|\x00+\z//g;
    $row->[5] =~ s/[^\w:]|(?<!:):(?!:)//g;
    $csv->print(select, $row);
}
$csv->eof or $csv->error_diag;
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