I've let Xcode upgrade a watchOS 1 app to watchOS 2. I don't see any app icons in the "My Watch" list in the Apple Watch companion app (which runs on the iPhone). I do see the icon for another app which still has a watchOS 1 app. Since the icons were always part of the Watch App and not the Extension, I don't see why moving the container for the Watch Extension as part of upgrading to watchOS 2 would affect this. I'm using the simulator, for what it's worth.
Anyone seeing icons in the Apple Watch Companion app for watchOS 2 apps?
I see the icons and sometimes not. And sometimes they appear but it takes alot of time.
When updating the app, I get a blank icon. If I remove from Watch, then add it back using the Watch app on the iPhone, the icon shows up.
mostly see the same as you described. Even on Xcode 7.0.1