Alright, so the sort of disclaimer on this whole Instructable is that you may freeze up you Xbee during the update process when changing settings, and modifying the xbee via XCTU. Don't worry, it is rare. But if you happen to run into this dead xbee situation here are the steps to try before ripping some hair out, and declaring your Xbee's time of death.
These steps we contributed by Cristof. Thanks to him, we have a solid step by step run down on how to attempt a fix.
1. Take the module out of the interface board.
2. Connect the interface board to the computer.
3. Open X-CTU make sure Baud Rate is set to 9600
4. Go to "Modem Configuration"
5. Put a check in the "Always update firmware" box
6. Select proper modem from drop down menu,
7. Select proper function set and firmware version
from drop down menus.
8. Click on the "Write" button. After a few seconds of
trying to read the modem, you will get an Info box
that says Action Needed. At this point, CAREFULLY
insert the module into the interface board.
9. You may get the info box again a short while after,
just use the reset button on the interface board.
Update: Well after letting this instructable soak for a while, some comments brought a missing piece to my attention. If you are working with an Xbee Explorer board that does not have a reset button, you can not complete the process. That won't do, so we have come up with a simple fix for you. Take a wire to jump a connection between RST, and GND. When it comes to the point that you need to reset (Hint this will work any time you need to reset.) just jump the two pins together, and you have reset the device! Good Luck friends.
Update 8/23 Thanks to reader kolment2003 a great recommendation to use a bread board, to switch for the Reset to Ground. This will allow a solid connection, and a reliable reset when you need it. Thanks kolment2003