I just installed several SmartWings shades and I have experienced the same issue. I am running HAOS on top of Proxmox with a HA SkyConnect passed through Proxmox to HAOS.
When I restarted Home Assistant, all of my Thread devices were disconnected. I was able to get them back by restarting the Matter Add-On in Home Assistant. Not sure if that will work going forward but it worked today.