I am having the same exact issue after I updated to BIOS 2305 on the ProArt Z-690 Creator WiFi board. I tried everything possible after scouring these forums and using MoKiChU's drivers. Still the same result.
I basically have to restart the PC twice in order for the two Thunderbolts to be seen. Cold boots = no Thunderbolt 4. Warm boot = Thunderbolt 4 is seen.
Asus is aware of my case and I've been waiting a week for a solution. Downgrading to BIOS 2204 can't happen as BIOS 2305 is locked for downgrades.