You can clear out the eMMC using the dd command. I also had this problem where if mainline OpenWrt U-Boot is installed on the eMMC, it completely ignores the SD card unless it fails to boot. By clearing the partitions OpenWrt is installed in, the problem resolved for me. In my case it was in /dev/mmcblk2p1-2 and I used dd if=/dev/zero of=/dev/mmcblkp2p1 bs=8M count=1 to clear out the OpenWrt installed in the eMMC. After doing this I was able to boot from the SD card I plugged into the device.
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