Another option would be split with capture brackets, like this

#!perl
use strict;
# create test file
open OUT,'>','line.txt' or die;
binmode OUT;
print OUT "Windows".chr(13).chr(10);
print OUT "Unix".chr(10);
print OUT "Windows".chr(13).chr(10);

open OUT,'>','copy.txt' or die;
binmode OUT;

open IN,'<','line.txt' or die;
binmode IN;
while (<IN>){
  my ($line,$eol) = split /([\015\012]+)/,$_;
  # process $line
  print OUT $line.$eol;
}
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