Hi sfeutrier,
I believe that your issue is caused from the bit 10 of pinmux register has been set.
Please apply the patch from the following thread to check if it could help for your case.
40hdr - SPI1 gpio padctl register bit[10] effect by gpiod tools in JP6 - #20 by KevinFFF
You can simply update the /boot/Image instead of reflashing the board to apply the change.