I have a problem just like yours. I have same model of xbee and my xctu is 6.3. Please tell me step by step how you solved it, I could not understand what you did to solve.
What I would do is open a terminal window on the same COM port but enable the break and assert RTS. Then hit the rest button on the interface board. deselect the break and issue a . A menu will come up. Pressing B will put you in bypass mode. Once in bypass mode, use the same steps as before to write the new firmware to the module.