I must have misunderstood the documentation but I was under the impression that any user changes to the PE generated ISRs would not be overwritten. However, my changes are being overwritten. For instance, I want to make changes to the PE_ISR(GPIO2_Interrupt) interrupt routine generated by PE. Is there something else I need to do so that these changes won't be overwritten?
Or better yet, define my own ISR function in another file outside of PE. Is there a way to communicate the name of my ISR function so that it gets added to the ROM vector table instead of the one generated by PE? My code copies the vector table to RAM so I could interject it then.