So I managed to make it so that the 'command' is now 'updateChangingKeys':

{"commands":[{"schemaName":"opencyto_preprocessing","queryName":"GatingSet","command":"updateChangingKeys","rows":[{"values":{"Id":1,"Name":"test","Path":"/home/ldashevs/Labkey/flowFiles/HVTN080/@files/assay/0880-M-080/6edd36458d6da212026ec7676b76e6f8","Description":"description","EntityId":"d200e809-e4ad-102f-b2d1-1f5d89162b6e","Created":"2013-07-03T21:16:36.000Z","container":"d200e809-e4ad-102f-b2d1-1f5d89162b6e"},"oldKeys":{"undefined":"ext-record-2"}}]}]}

Though, before calling commitChanges() on the store I had to manually go through the modified records and set their .phantom values to false:

                        new Ext.Button({
                            //disabled: true,
                            handler: function(){
                                var records = strGatingSet.getModifiedRecords();
                                Ext.each( records, function(record){
                                    record.phantom = false;
                                });
                                strGatingSet.commitChanges();
                            },
                            text: 'Update'
                        })

Still this gives my 'unathorized' 401 error.
What is there to do? Please, help!