Some things are bound according to order.
I.E. If you have controls assigned to move faders on the mixing console, and change the order of tracks on your mixing desk, insert a new track, etc, it can be confusing.
If you’ve bound things to specific plugin VST parameters, again, the plugin needs to be loaded, and instance order matters.
I.E. Say you have two instances of Reverence. Then you unload one, and load it back later. You might find that controls are now bound to the wrong instance of Reverence.
It takes a little practice to use this stuff well in projects that don’t have pretty strict templates.
For track-by track stuff that is frequently changing, opt for Quick Controls instead. Use the Generic Remotes for things that are pretty static in your workflow, and set up templates for that work flow.
Don’t be afraid to use many smaller Generic Remote maps that you can stack/enable/disable as needed (set the input to NONE when you want it out of the way). Build maps on the fly as you need them for the less ‘static’ tasks that’ll rarely be in the same order/position for different projects, or project stages.