ok, figured it out. By looking at a lot of other forms. Mostly this one below
https://www.jamf.com/jamf-nation/discussions/25692/high-sierra-10-13-encrypted-users-not-showing-at-filevault-login-screen
I needed to do the following to make it work with an AD account.
- first i ran
sudo sysadminctl -secureTokenStatus [username]
to make sure it was coming back as disabled.
Then i ran
sudo rm /var/db/.AppleSetupDone
Restart the computer. This gave me an admin with a secure token. With that i ran
sysadminctl -adminUser "$GUIAdmin" -adminPassword "$GUIAdminPw" -secureTokenOn "$username" -password "$user_password"
In this context, $username (and their password $user_password) is the user you want to provide a secure token to. The $GUIAdmin is an administrator that was created either via a DEP workflow or through the GUI. As has been explained to me, in order to provide a secure token to a user, the account you’re doing this from needs to have a secure token as well.
Thanks to babodee for the above
After that i restarted the mac and it didn't see the AD user. Even though now the user had the token and was no longer showing up as someone who couldn't unlock file vault.
Then with what @koalatee gave me i ran
sudo diskutil apfs updatePreboot /
and we were up and running.