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my %seen;
for my $i (reverse (0 .. @$ref-1)) {
...
    # and removes the last element if id already seen
    $ref->[$i] = pop @$ref if $seen{$ref->[$i]->{id}}++;
}

my %seen;
my $removed = 0;
...
    $seen{$item->{id}}++ ? $removed++ : ($ref->[$i-$removed] = $item);
}
splice @$ref,-$removed;