Use operation node-delete with one or more filters to delete service nodes.

Request 

<packet>
  <extension>
    <call>
      <plesk-multi-server>
        <node-delete>
          <filter-id>1</filter-id>
          <filter-ip>1.1.1.1</filter-ip>
          <filter-hostname>example.com</filter-hostname>
        </node-delete>
      </plesk-multi-server>
    </call>
  </extension>
</packet>

Response 

<packet>
  <extension>
    <call>
      <result>
        <status>ok</status>
        <plesk-multi-server>
          <node-delete/>
        </plesk-multi-server>
      </result>
    </call>
  </extension>
</packet>