Our company bought a couple of "Arduino.org" Zero pro boards and would like to turn these into "Zero" board until we are able to purchase genuine "Zero" boards in europe. Has anyone succeeded in using a ".org Zero pro" with the real Arduino 1.6.5 IDE?
I must warn you that changing the bootloader or following any other advice given here on a Arduino.org product may invalidate your warranty. So be aware that anything you try to do to "convert" your "Arduino.org Zero Pro" into an "Arduino Zero" is at your own risk and we do not recommend it.
To avoid misunderstandings, I'll repeat here again: Doing something wrong can damage your board and you may lose your money.
since the Arduino philosophy is based on open hardware and software, flashing the Arduino.cc Zero bootloader into the Arduino.org Zero Pro / M0 Pro won't absolutely void
your warranty. We encourage people to experiment with the Arduino.org hardware boards. Of course, you have to pay attention when managing the Board I/O because there are some differences between the board. For example in the Arduino.org Zero Pro/M0 Pro boards the PWM are D2…D13, in the Arduino.cc Zero are D3…D6, D8…D13, and, as reported from cmaglie, digital Pins 2 and 4 are inverted and our board doesn't have the ATN pin at all.
Please keep in mind that the Arduino.org support provides assistance just for issues encountered running the Arduino.org bootloader.