Ok, I tried to reproduce this with two H9000s but I didn't hear any clicks or other distortions. There are a couple of different ways to set this up though. Here's what I did:
* The two H9000s were connected by SPDIF over optical. It's possible to also connect them via SPDIF over RCA.
* One of the H9000s was the clock master, and the slave H9000 had its clock synchronized via a word clock cable.
Was your set-up different than this in some way?
Some other possibilities to keep in mind are:
* Not all algorithms run at 96K. If you're starting with a fresh session and you load an algorithm that's not supported at 96K, both the H9000 and Emote will warn you of this, but if you switch an existing session from 48K to 96K, you won't necessarily see that there's a problem if you're only looking at Emote.
* Some users have reported they needed to restart their H9000s with the SESSION and FXCHAINS buttons pressed to clear out the H9000s current state to get it to switch over to a different digital audio mode and/or a different sample rate when using digital audio. This has come up a few times with running digital audio at 96K.