i thought what was needed was to (A) delete matching lines in file...and (B) write the matching lines to another file. If instead you could read the file and produce two output files, one file for the matching lines, and one file for the rest (unmatched lines), then the objective can be achieved with a slight modification to matija code like so:

open(OUTPUT,">matchingfile.txt")||die;
open(OUTPUT2,">nonmatchingfile.txt")||die;
while (<>) {
  chomp;
  if(/what you want to match/) {
    print OUTPUT $_ . "\n";
  } else {
    print OUTPUT2 $_ . "\n";
  }
  print OUTPUT $_      # note no semicolon here...
  unless /whatever condition matches the patterns you want/;
}
close(OUTPUT)|| die "Could not close $!\n";
close(OUTPUT2)|| die "Could not close $!\n";
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...and run the prog like this: perl prog.pl <yourinputfile