atxmegaa1uxplainedpro switching between edbg and USB DFU

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After setting up the RTC driver with overflow interrupt (5ms period), I was able to add the other interrupts the application needs (external pin interrupts on 4 pins, only two interrupts can be active at a given time). Everything was working as expected using the edbg interface for programming and a teraterm window to view target USB transfers. I then used USB DFU to program the application and tried to run it. Since then, the external interrupts are not registering in the input pins. Is there a way to avoid this problem, did interrupt vector locations get erased or change due to using USB DFU?

 

I then erased the chip and went back to using edbg to program the board. The RTC interrupt triggers but not the external interrupts. The heartbeat LED is blinking on the eval board. Is it possible to safely switch between using USB DFU and EDBG? I have ordered new eval boards. I appreciate a response.