How about undoing some of those loops. If your file names are as consistent as they look from your example, this is a simpler way to do it

#!/usr/bin/perl
use strict;
use warnings;

# Read barcodes, and look for coresponding files to rename
my $dir = "/samplesA";
my $bcf = "/ID.txt";
open my $barcodelist, "<", $bcf or die "Can not open barcode file $bcf
+: $!\n";
while (my $line = <$barcodelist>) {
   chomp; 
   my ($id, $barcode) = split(/\t/,$line);
   # I like validating inputs
   warn "bad line at $.\n" unless $barcode =~/^[ACGT]+$/; 
   my $file = "$dir/sample_$barcode.fq";
   if (-e $file) {
     my $new = "$dir/$id.fq";
     rename $file, $new or die "Can't change $file to $new, $!\n";
   }
}
close $barcodelist;
[download]

Cheers,
R.