In my Waves SoundGrid setup between GLD and SQ5, I needed to manually set the SQ5 for 48K clock from its default of 96K. Works fine since then. The GLD is the master clock in my setup.
You are misunderstanding what you are changing. There is no way to change the clock speeds of the A&H consoles. They will ALWAYS run at their default clock speeds. When these consoles are connected to another device with a different clock speed, it’s the connection interface that will handle any needed conversion. In your case, it’s the Waves card that is handling the clock conversion, not the console itself.
You may be changing where the SQ console “looks” for it’s master clock (the Waves card instead of internal), but the console is still running at 96k.
In the OPs case, the Dante card will need to be set to 48k and it will handle the conversion. Depending on which device needs to be the master clock, they may also need to change the SQs master clock from internal to the Dante card. It’s probably best if the SQ is the master clock, meaning the SQ console’s clock is set to “Internal” and the SQ Dante card is set to “Preferred Leader” and “Sync with External” meaning it is synching with the SQ’s clock (the external device) instead of another Dante device. The second console’s Dante card should have the “Preferred Leader” option unselected.
