Duet 2 WiFi stuck in SAM-BA mode and MCU overheats after SPI firmware changes – unable to recover via JTAG/SWD

We are working on a custom firmware feature for Duet 2 WiFi, and after modifying the firmware to communicate with an external MCU via SPI using the expansion port (PB0, PB1, PB13, PA24), we encountered a critical issue on two different Duet 2 WiFi boards. A custom G-code command (M2000) was implemented to trigger SPI communication from within the firmware, which compiled and flashed successfully using bossac with the command -e -w -v -l -b Duet2CombinedFirmware.bin. However, immediately after flashing, both of the Duet 2 WiFi boards failed to boot normally and appeared only as SAM-BA USB devices on the PC. Additionally, the MCU began overheating rapidly even while idle. When attempting to reflash the official Duet2CombinedFirmware.bin, we received a Verify failed message with Page errors: 1021 and Byte errors: 377954, indicating a severe write or flash integrity issue. We attempted recovery through both SWD and JTAG using a J-Link, ensuring correct pin connections and testing with and without resistors R36, R49, and R52 populated, but results remained the same. The J-Link interface consistently reported "RESET (pin 15) high, but should be low", "Unexpected core ID: 0x00000000", and "TDO is constant high", preventing identification of the target. We verified that VTarget was correctly detected as 3.3V and all connections were sound. We believe the custom SPI firmware may have caused a hardware fault or internal lockup, possibly through misconfigured peripherals such as DMA or SPI. At this point, we are unsure whether the MCUs are permanently locked or physically damaged and would appreciate any suggestions on recovery, or confirmation whether MCU replacement is our only option.