I’m guessing that at some point you added a Thread device to the Google Thread Border Router using your Android smartphone, and that it’s now set as the default border router on your smartphone. Or you used different smartphones.
I’m just a beginner when it comes to Matter and Thread, but in my opinion, there shouldn’t be any issues with using multiple Thread networks, since the devices can communicate with each other via the Matter protocol.
Matter is the communication protocol.
Thread is the network environment.
It does cause issues if you have multiple thread networks. At least it did for me. Once I merged my two together (Apple Home and Aqara) things worked better
my understanding is that the Homey companion app uses whatever Thread credentials are on the Android phone. (according to ChatGPT searches). So this seems to point to using a different phone for that device? It is not clear (to me) if this thred credential is shared to your other Android devices. I do know that there is only the nuclear option of a phone reset to get rid of a stored one.
(I am still persuing an OTBR in docker with no other Border Router on the network for Homey-SHS. I will have to commission once using Home Assistant to get the credentials onto the phone)