I’ll second this as a pain point having now done the same thing. The tv remote needs to be a valid and consistent input for navigating menus before selecting a computer to connect to (the first screen of the link app)

The controller binding interface is really non-obvious here and you can pretty easily rebind inputs away from the back/confirm actions trying to escape that screen. It looks like the only way to recover is then to delete and reinstall the link app because the remote is not recognized as an input while a controller is connected and the controller binding can’t be reset while it is not paired.

That's what I ended up doing.

I had to do the exact same thing. Clearly an oversight on the developer's part.

This is indeed a problem and made me believe I had bought a controller for nothing.

I also messed up the controller initial setup and after that neither the apple TV remote, nor the iOS remote app and not even a bluetooth keyboard connected to the apple TV work on the link app while the controller is also connected meaning you can't fix the controller setup.

Thankfully @Perith's suggestion of re-installing steam link allowed me to configure the controller from scratch and work around this bug.

This is still an issue 2 years later. Has steam given up on supporting remote play?

Happened to me just now. Had to reinstall steamlink app