$ cat unixordos.pl
use strict;
use warnings;
my $fh = undef;
open($fh, "<", "foo.txt") or die "failed to open 'foo.txt':$!";

while (my $line = <$fh>) {
  $line =~ s/\r\n/\n/g;
  chomp $line;
  ($line =~ m/^\d+$/)
    ? print qq{number ok:"$line"}
    : print qq{number error:"$line"};
  print "\n";
}
close($fh) or die "failed to close 'foo.txt':$!";
__END__
$ echo -e "123\n456\n789" > foo.txt
$ perl unixordos.pl
number ok:"123"
number ok:"456"
number ok:"789"
$ unix2dos foo.txt
unix2dos: converting file foo.txt to DOS format ...
$ perl unixordos.pl
number ok:"123"
number ok:"456"
number ok:"789"
$
[download]

I guess a s/\r\n/\n/g followed by chomp would do it

That substitution is exactly what the crlf PerlIO layer is doing (on input). The layer is by default in effect when you're on Windows (which is why you don't have the problem with Windows' files on Windows :)

In other words, you could also do

open($fh, "<:crlf", "foo.txt") or die "failed to open 'foo.txt':$!";
[download]

It should work AFAIK.

It too converts single CR to LF (mac format?)

Rule One: Do not act incautiously when confronting a little bald wrinkly smiling man.