Something like this...

($small_file, $big_file) = @ARGV;

open SMALL, $small_file;
while(<SMALL>)
{
    $id_to_remove=$_; chomp $id_to_remove;
    $hash_to_remove{$id_to_remove} = $id_to_remove;
}
close SMALL;

open BIG, $big_file;
while(<BIG>)
{
    $id_to_check=$_; chomp $id_to_check;
    if(not exists $hash_to_remove{$id_to_check})
    {print $id_to_check."\n";}
}
close BIG;
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