Delete old rules that are in the database. Best used in a hook_update_N() implementation.

clean-rules.php

<?php

  $type = 'rules_config';
  $query = new EntityFieldQuery();
  $rules = $query->entityCondition('entity_type', $type)
    ->execute();

  if (!$rules) {
    return;
  }

  rules_config_delete(array_keys($rules[$type]));