If you want to keep a shuffle persistent, I would supply the "shuffle order" as a config file and also allow the option of easily creating a new shuffle:

use strict;
use List::Util 'shuffle';
use GetOpt::Long;

GetOptions(
...
);

my @items = get_all_items;
my @shuffle = shuffle 0..$#items;
if ($save_shuffle_sequence) {
    open my $fh, ">", $save_shuffle_sequence
        or die "Couldn't save shuffle sequence to '$save_shuffle_seque
+nce': $!";
    print {$fh} "@shuffle";
};
if ($load_shuffle_sequence) {
    open my $fh, "<", $load_shuffle_sequence
        or die "Couldn't load shuffle sequence from '$load_shuffle_seq
+uence': $!";
    @shuffle = map { split /\s+/ }, <$fh>;
};

my @shuffled_items = @items[ @shuffle ];
my @other_items_shuffled_in_parallel = @other_items[ @shuffle ];
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