Hi,
I have observed the same modification of extlinux.conf after update, without problem in my case: there
It happens with update to JetPack 4.4 - L4T R32.4.3 production release
New cboot version doesn’t add “root=…” parameter (and other things from cbo.dtb) from CBO partition to kernel command string, so while bootloader updates extlinux.conf file (/boot/extlinux/extlinux.conf) is parsed to add this parameters with APPEND. In your case something go wrong and parameter is missing.
How to edit extlinux.conf from initramfs, where Xavier is stuck in case of error is a good question :(.