I’ve seen the issue you’re describing when I added a SkyConnect OTBR to my existing Apple Thread network. I then created a new standalone Thread network with SkyConnect OTBR and migrated all my ~30 Homekit devices to this new Thread network.
What I didn’t know by then is that all these devices will vanish from their iOS apps, as iOS only searches the (now empty) Apple Thread network for devices. I now cannot adjust the temperature offset of my TRVs anymore, upgrade the firmware, adjust sensitivity settings on my motion detectors etc, because this can only be done from the iOS apps by Eve/Nanoleaf/… and not from the Homekit integration in HA.
I’m not willing to reset all devices and recreate them in HA, as I would need to rewrite all my existing automations.
My biggest wish for HA is therefor either a way to merge Thread networks, to let iOS discover/join a OTBR-Thread network or a way to seamlessly transfer a device from one Thread network to the other without having to reset&recreate it.
Also I wonder how and when I will be able to support my existing OTBR Thread network with a second border router so a single HA restart doesn’t reset the entire network – as it takes 5-10 minutes until it’s up and running again (end devices connecting to router devices connecting to router devices connecting to router devices to finally the HA border router).