Now that I've added a HomePod I'm finally getting around to configuring HomeKit with all of my devices. One Hue Bridge was no sweat but I have a second Bridge at a far end of the house. This Bridge refused to associate with HomeKit. I’ve left it that way for over a year but now I want everything in HomeKit with Siri control.
The root of the problem was caused by my network configuration. I had one Bridge (the fully HomeKit friendly one) connected directly to a wireless hot spot. The second Hue Bridge (the bad actor) was connected to another router that was really just an Ethernet switch on top of the main network. This forced the second Hue Bridge onto a different subnet, thus making it unavailable to HomeKit and the Home app.
So, if you have Hue bridges that don’t all get along, get them connected through WiFi instead of direct ethernet switch. See if that fixes it.