Anal-retentive comments: I think you meant $next, not next. You forgot to show us how $next was set.

Given the way you're processing the file, I think you need to include a state indicator.

my $changed = 0;

foreach $line (@lines)
{
  if ($line =~m/^SY /)
  {
    if ( $changed == 0 )
      {
        $line    =~ s/^SY/CN/)
        $changed =  1;
      }
    else     
      {
        $line    =~ s/^SY/  /;
        $changed =  0;
      }
  }
  else
  { $changed = 0; }
}
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There are terser ways of representing this, but I think this is readable. (It is untested, be warned!)