Hello,

You are correct that you can use analog, digital (ADAT/AES), USB, and expansion cards simultaneously. There is not a particular benefit to using one or the other, these options allow the user to integrate the H9000 into their system however it suits them. I personally use analog, ADAT, and Dante, with many different configurations depending on the work I am doing.

The PTHD card will give you an additional 32 channels of I/O using the PTHD format. These channels can be used via the 4 FX chains in various routing methods. Again, this all depends on how you would like to use it. You can use many effects in parallel within an FX Chain, or 1 stereo bus, etc.

Some more information about your use case and how many channels of audio you would like to process using the H9000 would help me in suggesting some setup options for you.

Your AES configuration may not be working anymore if you changed your clocking configuration. 

You should be able to connect 1 port of the HDX to the Aurora, and another port to the H9000 Primary port. You can continue to use Word clock for the clocking config, just set the H9000 clock source to Word Clock.

Additional information about the PTHD card setup can be found here: https://cdn.eventideaudio.com/manuals/h9000/2.2.11/content/expansions/protools.html

Let me know if that helps.