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Old 7th January 2020
  #4
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Ok, gotchya.

The way you're doing it, you're mapping them globally, not in focus mode.
The two mapping modes in S1 are global and focus, but it's easier to think of global as 'static' and focus as 'dynamic'.
When you pick something using the 'Assign to' method, it's mapping them statically, ie they won't release to be mapped to new parameters in another plug.

This kind of link is confirmed by a blue arrow between controller name and parameter name.

You want to do it so there is a yellow arrow between the two, which confirms that as you move to different plugs the mappings will follow dynamically, updating to each new plug as you move through them.

To do this, only use the External devices panel to define the hardware knobs and faders. You need to unassign all the controls, start over, only use the External devices panel to create the physical control chart.

You can either unassign controls by right clicking again in the External devices panel and choosing unassign, or just move a hardware control, check the box at top left of the arrange window to see the current link, and then click the coloured arrow between the control name and parameters name so it goes dark grey.
Now it's unlinked.

From now on, you will link using the same method as you just used to unassign (box at top left), or by using the same feature found by clicking the little cog icon to top right of a plugin gui (next to the drop down box that shows the name of the hardware device currently assigned to its control).
Either of these methods can be used regardless of what functions you're mapping.

Now you'll see straight away by checking the arrow colour whether you've hard-wired a control (blue arrow) or whether it's available to be mapped to other things too (yellow arrow).
This will solve any issues you have with plug control and other parameters.
It's only solving half the problem though.

As you say, because the S1 console only shows channels (ie things that pass audio), not tracks, you won't see any controls there for a midi (instrument) track until you've inserted a vsti, then you'll see that vsti's audio channel/s in the console.
I have a suspicion that regardless of how you've mapped your controls, whenever you remove an instrument, the links for it will be broken, because the link was made with instrument-specific parameters (its audio outputs) and not a pre-existing mixer channel.

What you want to try and do is use those facts in your favour, by mapping the vsti controls (including output channel controls) dynamically.
I don't know if this is possible but I'll have a play in a minute.