Martin, you can always boot up from the on module SPI (that is the standard way how iMX6 Rex boots) and then just update the env variables in uBoot. Here you can find default variables: http://www.imx6rex.com/software/how-to-uboot-compile-flash-update/#printenv_examples
You can see there the thing like: “mmc dev 1; ext2load mmc 1 0×10800000 uImage-gpu 3916636″ and you will need to update it based on where your sd card is plugged in. You also will need to update “root=/dev/mmcblk0p1″. I am not at the office, so I can not exactly test what values should be there, but I am sure you can figure it out.
Hope it helps, Robert
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