Xbee configuration with X-CTU on linux
Most probably, XCTU would not be able to get the correct COM port to which your Xbee is being attached or otherwise you might have bricked your Xbee.Iu would rather suggest to test you Xbee on windows and find out that you hadn't bricked it.

The other way is to use Hardware reset for your Xbee. You must probably short reset pin with that of VCC or GND (I am not very sure with respect to this.) But this is a sure short way to reset your Xbee.

You can also use a serial emulator for the same like minicom or screen.If using minicom, first find out to which port you had connected your Xbee, probably it will be something like /dev/ttyUSB0 (use dmesg to find out). The use sudo minicom -s , under Serial Port Setup --&gt; A. Serial device , edit it to /dev/ttyUSB0 and change baud rate to 9600.Now save this, then Save as DFL, then exit. A new screen will open. with 


  Cntrl+a then z, turn Local Echo ON.


Then write "+++",and don't press enter, if it revert you back with OK,then your Xbee is still alive or otherwise, use hardware reset. Probably as per your provided info, i think, you might be doing something wrong in providing softlink.

Also have a look at this page: Recovery procedure for Digi RF products. It might help you out.