This message was posted on behalf of Intel Corporation
I'm not sure I completely understood how you want to trigger the ISR. How exactly would you like to activate the interrupt? If what you'd like to do is to set, let's say, pin 6 on the mraa side to receive an interrupt and the mcu part to send the trigger signal, then no, this can't be done, the pins can either be accessed from the Atom CPU or from the Quark MCU but not from both on the same time.
If instead what you'd like to do is to use, let's say, pin 3 on the MCU for the trigger and pin 6 on the CPU for the interrupt, then you can wire them together and you will be able to trigger an interrupt.
As I mentioned, I'm not sure I'm following how you're setting up the interrupt, please correct me if I'm wrong. What you are currently doing is setting up an interrupt on the MCU on pin 14 and when that interrupt is triggered you check for either turn on or off pin 46. On the CPU side you set an interrupt on pin 32 (MCU pin 46) and wait for it to be triggered from the MCU interrupt, am I right? If so, then this wouldn’t work because of the reason I mentioned above, the MCU and the CPU can't interact with the same pin at the same time.