oh, such a long time from this post ... and still have not found an answer on the Internet. So after a few hours ... no, no, not that, came up with solutin
var jsTreeId = '#jstree';
var jsTreeSelectedItemId = 5;
var selectedNode = $('#node_'+jsTreeSelectedItemId);
var parentNode = $.jstree._reference(jsTreeId)._get_parent(selectedNode);
// , node , node ajax-, , ,
var newSelectId = 9; // or from ajax call
// call the refresh function, which is asnyc
$.jstree._reference(jsTreeId).refresh(parentNode);
// set the magic "to_select" variable with an array of node ids to be selected
// note: this must be set after refresh is called, otherwise won't work
$.jstree._reference(jsTreeId).data.ui.to_select = ['