If you want to replace existing node type definition, you should pass ExtendedNodeTypeManager.REPLACE_IF_EXISTS as a second parameter for the method ExtendedNodeTypeManager.registerNodeType.

ExtendedNodeTypeManager nodeTypeManager = (ExtendedNodeTypeManager) session.getWorkspace()

                                                                           .getNodeTypeManager();

InputStream is = MyClass.class.getResourceAsStream("mynodetypes.xml");

.....

nodeTypeManager.registerNodeTypes(is,ExtendedNodeTypeManager.REPLACE_IF_EXISTS );