Can you try this version and report its output.

#!/usr/bin/perl
use strict;
use warnings;
opendir(DIR, "/samplesA") or die "Can not open folder, $!\n";
my @files = readdir(DIR);
closedir (DIR);
open my $barcodes, "<", "/ID.txt" or die "Can not open barcode file, $
+!\n";
my @lines=(<$barcodes>);
close $barcodes;

for my $file (@files) {
   next unless $file =~ m/fq$/;
   foreach my $line (@lines) {
      chomp $line;
      my ($id, $barcode) = split(/\t/,$line);
      if ($file =~ m/$barcode/) {
         my $new = $file;
         $new =~ s/sample_$barcode/$id/;
         rename ($file, $new) or die "Can not change $file to $new, $!
+\n";
      }
   }
}
[download]

Perhaps strict and warnings will help

Cheers,
R.