Configuring Matter/Thread with a Skyconnect on a working system

My HA system is solid, and I am running both Zigbee and ZWave with separate dongles. The Zigbee dongle is an EFR32 one from Tube and the ZWave one is an HUSBZB-1. They are working well, and I am thinking about exploring Thread/Matter.

I purchased a Skyconnect a while back and would like to add that to the system as a dedicated Thread/Matter device. My concern is that if it needs to be flashed for the scenario, plugging it in might break the current system, as HA would see two Zigbee coordinators.

Is that a realistic concern? What are the best practices for doing this? Should I use another tool to flash the SkyConnect outside of HA to avoid the issue? I can do that, but need instructions. Alternatively, if I flash in HA, can I be confident that it won’t break my initial config when I plug it in?

TIA in advance for any ideas and perspectives.

I think you should be OK, but when you plug in the SkyConnect, goto UI->Settings->Hardare and you should see the Home Assistant SkyConnect, then click on CONFIGURE, and it will ask you whether you want to set it up for Zigbee or Thread.

You should be able to flash a thread only firmware on another conputer, like your workstation.
Today it is done in a compatible browser, like Google.

Thank you both for the response. Indeed, once you plug in the SkyConnect, HA recognizes it and asks about desired config as pictured by @wmaker. I chose thread and everything just worked. TY again!