If the modules are not on the same network anymore, there is nothing you will be able to do over-the-air via XCTU. You will need physical access to the modules, either to connect them to XCTU
(or to use the Commissioning Pushbutton on ZigBee devices)
http://www.digi.com/resources/documentation/DigiDocs/90002002/default.htm#reference/r_900hp_commissioning_pushbutton_.htm
http://www.digi.com/resources/documentation/DigiDocs/90002002/default.htm#reference/r_cmd_cb.htm