I'm not sure what's going on, but within the same night I was using Steam Link on my Pi 3B I have lost Steam Controller support, but the weird thing is it's not completely gone, rather it seems to be broken.
I have tried restoring the firmware and using a wired connection and trying it on a Mac and Windows PC and it weirdly seems to not work on my Mac, but works fine on my Windows PC.

That aside, trying to connect it to the Pi at all results in the Link app identifying the controller as "Generic". There is no mouse control from touchpad, and it asks to configure the controls if they weren't already. Connecting to Steam then renders the controller useless. It doesn't even show up or enumerate on the host PC. I have two controllers plugged in, and the 8BitDo SNES 30+ is working fine. I'm sure a DualShock 4 controller will also work, and I haven't tested my 2nd Steam Controller yet, but this is quite bizarre.
It also works fine on Android on the latest build. Switching to beta changed nothing.

One small quirk, I AM using this on OSMC with the launcher, but before this Steam Link worked completely and totally fine. I even reinstalled the app and deleted the steam link directory but it didn't do anything.