I've never tried it with two controllers. I only have one Elite Controller 2.
I was able to reproduce the problem where I did the whole restart + resync fix, then I turn off the console, then turn it back on with quick resume. It switches me then to blue controller and vibration is gone.
At least for one controller, the consistent fix is doing the restarts + resync and that forces it to select the main controller (red). It'll start showing up blue and green for me after the resync which might also be part of the problem in the code. (Seems like it detects there are other controllers present?)
For the Devs reading, it doesn't seem to be quick resume as the issue because I can restart the console, then go back into the game with quick resume, resync and it seems to work. It seems like the restarting clears some sort of memory cache for the controller and then resyncing forces it to be cleared.