Hello Christian,
The possible reason of the fact that the processor becomes damaged on the second board after pressing the POR button is as follows. Here I call "first" the board that is connected to the USB Host bus through the OpenSDA connector and distributes power and GPIO signals to the "second" board.
Please refer to the Sheet 4 of the i.MX RT1050 EVK board schematic. As it can be seen, pressing the SW3 POR button switches off the U3 DCDC converter, that produces the DCDC_3V3 voltage, that is the main system power supply voltage. Thus, pressing and releasing the SW3 button completely power cycles the board.
So, when you press and hold the SW3 button, the board power is completely switched off, including the GPIO power banks. At the same time, the 3.3V supply voltage from the first board is directly (even without any current limiting resistors) is applied to some GPIOs of the second board's processor. In this situation, the GPIO circuits of the second board's processor become irreversibly damaged.
Also, applying the supply voltage directly to the GPIO pins is not a good practice. Some series current limiting resistors (at least of 1kOhm) should be used in that case.
Best Regards,
Artur