The lwp-download script actually checks for existing files and then prompts you before it overwrites them. Unfortunately that part of the program stopped working in the download subroutine.

# Check if the file is already present
          if (-f $file && -t) {
          $shown = 1;
          print "Overwrite $file? [y] ";
          my $ans = <STDIN>;
          unless (defined($ans) && $ans =~ /^y?\n/)                   
+           {
              if (defined $ans) {
              print "Ok, aborting.\n";
              }
              else {
              print "\nAborting.\n";
              }
              exit 1;
          }
          $shown = 0;
          }
          else {
          print "Saving to '$file'...\n";
          }
[download]

I will try your suggestion to use system instead of the subroutine.