Rescue image is located in NOR, so content of the eMMC has no efect. Once you boot your Omnia (you can use omnia-initramfs-zimage from the link bellow), erase partitions mtd0 and mtd1 and write into them files from https://repo.turris.cz/omnia/nor_fw/
uboot-turris-omnia-spl.kwb to /dev/mtd0
omnia-initramfs-zimage to /dev/mtd1