*Update, i worked around this by placing a copy of the files inside of the nvme and it seems to have worked.
found this idea here: https://forums.developer.nvidia.com/t/cboot-in-32-7-2-fails-to-read-extlinux-conf/214017/4
previous post's text before update
We want to boot from the emmc, we have no intention of booting from the nvme, but while booting it seems to attempt to look for the extlinux.conf file inside the nvme and when it doesn’t find it it just defaults and never looks for it in the emmc.