Hey Nathanael. Just to start I am a user and I do not work for DAD. Your issue is that the cards that you pulled from your MTRX are not compatible with the AX64. The Avid branded cards have firmware on it to block them from being interchangeable with the DAD chassis. You would either need to buy DAD cards and get rid of the Avid cards. Or buy the new Avid MTRX chassis with thunderbolt option to repurpose your old MTRX cards.
It sucks that they are not interchangeable, because physically they are the same cards. But this is how Avid is making their money off of the hardware.
If you still have your MTRX Chassis, pop your cards back in there. Route your cards I/o via either Madi or Dante to your AX64 until you sort things out. This will get you running again. Just make sure the MTRX is clocked to the AX64.