How to conditionally update and import nodes using Migrate?
OK, at least now I know, that splitting migration into two with filtered rows works just fine. prepareRow function looks like this:

public function prepareRow($row) {
  // If node exists on destination
  if ($node = node_load($row-&gt;nid)) {
    // Use the metatdata wrapper to pull values
    $node_wrapper = entity_metadata_wrapper('node', $node);
    // If destination title is the same as source title
    if ($node_wrapper-&gt;label() == $row-&gt;title) {
      return TRUE;
    }
    else {
      return FALSE;
    }
  }
  else {
    return FALSE;
  }
}