Please download the rootfs filesystem
wget https://www.nxp.com/lgfiles/sdk/lsdk2004/rootfs_lsdk2004_ubuntu_main_arm64.tgz
Please deploy images to SD card on your host.
$ flex-installer -b bootpartition_arm64_lts_5.4.tgz -r rootfs_lsdk2004_ubuntu_main_arm64.tgz -f firmware_ls1046ardb_uboot_sdboot.img -d /dev/sdx
I didn't reproduce your problem with LSDK 2004 pre-built images.
Please download prebuilt bootpartition and rootfs
wget https://www.nxp.com/lgfiles/sdk/lsdk2004/bootpartition_LS_arm64_lts_5.4.tgz
wget https://www.nxp.com/lgfiles/sdk/lsdk2004/rootfs_lsdk2004_ubuntu_main_arm64.tgz
Please deploy images to SD card on your host, then test whether this problem exists on your target board.
$ flex-installer -b bootpartition_LS_arm64_lts_5.4.tgz -r rootfs_lsdk2004_ubuntu_main_arm64.tgz -d /dev/sdx