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my $x = rand(65536);
foreach (@lines) {
...
   print $fh_out $_;
   $x = ($x + 1) % 65536;
}

my $x = 0;
foreach (@lines) {
   open(my $fh_out, '>', sprintf('prefix.%04d.txt', $x++)) or die;
   print $fh_out $_;
}

while (<$fh_in>) {
   open(my $fh, '>', sprintf('prefix.%04d.txt', $.)) or die;
   print $fh_out $_;
}