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The Apogee Big Ben has a led in the front panel for each of the 8 BNC word-clock connections which is lit up when the device atttached is properly terminated. The H9000 is not lit up and it shows as not terminated either if you turn on the internal termination from the clock menu of the unit nor if you attach the little physical termination dongle with a T-shaped adapter at the connection to the Big Ben.
This indicates under-termination. Nonetheless, the H9000 may still be correctly locked to the word clock. I read this Apogee tech note on the Big Ben: https://apogeedigital.com/pdf/bigben_termination.pdf – it is possible that we also have the same issue as MOTU equipment, but in any case we are going to try to get hold of a Big Ben and will get to the bottom of this.
One thing that I still do not understand is why the H9000 has to be booted up first and then "synced" by the computer (DAW) whereas any other device utilizing word-clock is just flowlessly synced by the master clock, following any S/R change without problems. Does this have anything to do with the termination problem?
The audio mute issue is almost certainly unrelated to the word clock termination. The problem is the way that the asynchronous USB audio connection works. There's no way for the H9000 to tell the computer to resync itself when the clock changes.
It should be possible to manage this using the CoreAudio aggregate device. If you set the RME to be the "Clock Source" in the aggregate device in Audio/MIDI Setup, then you should be able to change the sample rate of the H9000 device in AMS independently of the sample rate of the aggregate device. So, if you get the USB mute problem, change the sample rate of the H9000 device (NOT the aggregate device!) to 44.1 and back to 48 again.
I've attached a couple of screen shots to illustrate what I'm describing. In my example the two devices are MG-XU (which is my mixer's built in audio interface) and Eventide Dice (which is my H9000 – it is an older hardware rev without USB). I have set the the aggregate device clock source to MG-XU (i.e. not my H9000). My aggregate device's sample rate is 48kHz, but as you can see, the H9000's sample rate is 44.1kHz. I can change the H9000's rate without affecting the sample rate of the aggregate device.