hello evchupriyanov,
here’re roughly steps for your reference,
(1) you may put the device into recovery, execute below to create the base image.
$ sudo ./tools/kernel_flash/l4t_initrd_flash.sh --network usb0 --no-flash jetson-xavier-nx-devkit-emmc internal.
(2) then, please replace the default eks imagem i.e. eks_t194.img with yours.
please using the same key with, -i ekb.key to generate an image blob.
$ sudo ROOTFS_ENC=1 ./tools/kernel_flash/l4t_initrd_flash.sh -i ./ekb.key --network usb0 --no-flash --external-device nvme0n1p1 -c ./tools/kernel_flash/flash_l4t_nvme_rootfs_enc.xml --external-only --append jetson-xavier-nx-devkit-emmc external
(3) finally, put the device into recovery and then run below.
$ sudo ./tools/kernel_flash/l4t_initrd_flash.sh --flash-only --network usb0