I've "bricked" a series 1 and was able to recover it by a combination of the following. YMMV since you have a different version, but worth a try.
Obvious setting - the port speed. Stick with 9600 till everything works.
If your original firmware is much (much) older than the latest release - try to flash a less newer release from X-CTU first. Then, step up to the latest firmware.
If the XBee is not responding to AT commands. Change your PC (assuming Windows) port settings to use HARDWARE FLOW CONTROL (control panel, device manager, ports, COMx). Unplug and replug the XBee USB explorer. Start X-CTU. Don't try to test the port, just go into MODEM CONFIG tab, leave the firmware option UNCHECKED at first, click the RESTORE button. This should recover the XBee to a factory default. Then step up to an interim (less newer) firmware release and check the ALWAYS UPDATE FIRMWARE box, click WRITE. Do it twice. Then select the latest firmware release. Click WRITE. Uncheck the firmware box. Click WRITE. This should get the XBee alive again. Then you may make config changes as required, just watch that port speed, I've not been able to get my Series 1 higher than 9600 with any level of reliability.