I've had a very reliable setup for several years, noticed many issues around the time updated iOS 18.
1) ATV via Ethernet has always been the best standard for a reliable thread network on HomeKit. 18 released the ability to prefer a hub, but prior to this I had my HomePods on smart switches power cycling nightly to insure they were ALWAYS on and ethernet Apple TV's. the Apple TV has a much more powerful CPU, and that seems to be required with larger or more complex setups. I suspect when people unplug the Ethernet (or plug it in) it is simply loosing the hub and causing it to rebuild the thread network from scratch which resolves any issues.
2) I've noticed that the iOS version and updates are very temperamental after updating to 18. If ANY device is outdated (iPhone, mac, Apple TV, iPad, HomePod etc..) then I've noticed constant issues. Another thing I've seen is that the hub will prefer (if on auto select hub) the latest updated hub over any other hub. This also explains why people are getting a new phone, Mac, Apple TV etc... and it "fixes" it, I'm guessing it simply received the latest update. I don't know why they can't have different versions, but this has fixed it for me 3 times now, then rebuild the thread network and I'm back until the next update.
2 things I to try that should recover the your thread network.
1) update all your devices
2) In home app > home settings > home hubs & bridges, change the hub to different hub (or power cycle the current hub) to trigger a rebuild of the thread network. Give it 10 min, but can be up to a full hr to complete. For anything not responding after 1hr, you power cycle that specific device(s) they should all add back in fine.
PS, for those with Nanoleaf products. I've done extensive research. They are complete crap now, my old thread only bulbs still work great but any of the new "matter" devices are awful and can even mess up OTHER devices on my your thread network. A few tips for Nanoleaf stuff...
- You can use them in the Nanoleaf app (without matter integration) OR you can add in home app and not complete the setup in Nanoleaf app. But if you try to let both home app AND Nanoleaf app have full control of the bulbs at the same time, they will wreck your network. So either choose limited features home app, or choose Nanoleaf and loose the ability to use voice commands/automations app control.
- If you can't adopt, you may need to hard reset them. Turn them on/off 5 times for bulbs, hold power for light strips etc.. should blink several times red and reset. If you see device is already there, the ID is 3 characters and likely matches an existing IS, turning off the other bulb or device with the same ID while setting it up will work, but note those devices will likely get lose and mixed up.