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Glad to hear that you were able to get this working, I’m not sure what the issue you were having was. On the H9000, you can use all of the I/O from your analog, digital, USB, and expansion cards simultaneously, so there is no issue with using your AES and Pro Tools expansion card I/O at the same time. All of the I/O is configured with your FX Chains, so a simple example would be using AES 1+2 for FX Chain 1, and PT|HD 1+2 for FX Chain 2, but these can be configured however you like.
With 1 HDX card your total I/O is 64 channels, 32 channels per DigiLink port. If you already have 2 devices connected to your system, then you can choose to only use 16 inputs on one of the devices and have the H9000 daisy chained to this device, but this would limit you to only having 16 channels of I/O on your H9000’s Pro Tools expansion card. The Secondary port of the 1st HD device would connect to the Primary port of the expansion card to set up the daisy chain, or vice-versa if you wanted the H9000 to be the 1st device. You would also need to set the PT|HD card to be in 16-channel mode.
You will need to configure the clocking on all of your devices for this to work correctly. This can be done using Word Clock, or you can setup a LoopSync between your other HD devices and the H9000’s Pro Tools expansion card.
Let me know if you need any further assistance.