I have the 'regular' BE98 (with 2x 5GHz radios) as opposed to the BE98 'Pro' with it's 2x 6GHz radios.
The 6GHz band should only have a slightly weaker range than the 5GHz in theory, however, I find that in practice that makes a big difference for more distant stations.
I've only ever ran a slightly older RT-AX88U Pro with a RP-AX58 in an AI mesh set up (both are up for sale in the for sale section!) but I haven't used the BE98 in an AI Mesh. From what I know of the BE98, one of the 5 GHz radios is dedicated to wireless backhaul whereas on the 'Pro' it's one of the 6GHz radios*. As such, if you're already seeing a performance drop on the 6GHz band, your AI Mesh is already compromised.
For me, a couple of questions:
1) If your AX11000 set up was rock solid before the latest firmware upgrade, why not roll-back to the stable firmware, feedback to ASUS and await a further update? Or, if it was rock solid previously, could you not stay on that last firmware regardless of further updates?
2) With the BE98 'Pro' dedicating a 6GHz radio to backhaul*, are you able to place them in better positions where they can achieve a higher throughput?
*I haven't tried AI Mesh with my BE98 so I don't know if it is possible to select a specific radio for backhaul.