At this stage I want to mention some ideas and consequences about using VMC as a Control Surface. It is the same for all Digital Mixers.
"Native" Control Surfaces are just physical controls which send a signal to the DAW when operated and sometime provide feedback (lit LEDs, move faders, show something on display). Important is that each control send exactly one signal. There is no "hardware modes" for controls, all "different layers" are programmed in software.
Digital Mixers (in native mode, some have "DAW controlling" mode where they behave as Control Surfaces) see things from another perspective. Hardware controls are not sending signals to outside, they somehow operated Mixer internal parameters. And these mixer parameters are exposed to the outside world. While that sounds almost the same as with Control Surfaces, the result is significantly different:
1) when controls are switched to another layer, they start to modify another set of parameters. The control is still the same, but the signal from it from the DAW perspective is different.
2) when DAW is changing some parameter, the mixer "broadcast" the change. Not only to the controls (if it happened they control these parameters in current layout), but also back to the DAW. This you have already observed and we had to implement a workaround.
Brute force approach can be as simple as mapping existing Mixer parameters with DAW parameters and keep them in sync. In that case it does not matter which parameters are currently exposed to hardware controls. Unfortunately, that does not work well, at least with Sonar:
a) to load all settings, mixers use some special bulk mode. In assumption that does not happened often, no problem it takes quite some time, the whole information is transfered every time. That does not match DAW controller schema: when you change WAI, select different plug-in, etc. you do want update a big part of the configuration. But not the whole configuration, as for example at the project loading. That can delay reaction on WAI movement, to transfer the whole set of parameters, even when physical controls at the moment are in different layout.
b) monitoring a huge number of parameters does not come for free inside Sonar. Surface plug-in (AZ Controller) pools 13 times per second for each such parameter.
And so general approach is try to LIMIT which parameters are monitored and synced with the mixer to the set of parameters currently assigned to the hardware controls. F.e. when faders control Volume, monitor and sync volume. When they control send volume, monitor and sync send volume (but no longer monitor/sync track volume!). There are 2 approaches to achieve that, the availability depends from the mixer and so you will have to decide:
1) Much simpler to program. Let hardware controls control always the same mixer parameters. F.e. let faders always bound to the (Mixer!) channel volumes. To still allow control something else in Sonar (send volumes, plug-in parameters, etc.), the software need ANY signal to switch the mode. So any button which does not switch what faders are controlling, but modify some (mixer) parameter and so inform the DAW it is pressed. F.e. HPF enable on channel 14... Really the parameter inside Mixer make absolutely no sense for the DAW. Unfortunately, that is not aways possible. F.e. there is no such buttons and/or selecting particular channel also select it inside the mixer, and so some knobs control different parameters (like in Yamaha mixer I have configured before). So the option number:
2) Much tricky then the first one... If Mixer report about control layout switch (Yamaha does), the DAW can detect hardware controls are going to send/react on different messages and adopt.
You have experience with your device, I think you can find what is possible in your case much faster then me (reading I must admit rather bad written documentation).
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I will try to find some time tomorrow (I am not at home these weeks) to write an example with mute. But we will hit the same problem as with pan if I do that strait (simple). You can notice that volume and mute (and other parameters) for the same channel have similarities... I will have to compose the feedback for faders, mute, pan (?), etc. into one SysEx.
BTW. Are all "channel buttons" on the device have LEDs? I mean do we need the feedback for all of them? Also since you already know the answer: how you control pan? I do not see any per strip encoders on picture (I know that I can look into documentation... but)