Duplicate Sonos zones usually point to discovery on the network side, while a speaker that still works in the Sonos app but no longer appears in Roon is often a sign that Roon is seeing a different network path than Sonos is. A couple of things will help us sort out which side is drifting.
Could you confirm whether your Roon Server is wired or on WiFi, and whether you have any mesh nodes, managed switches, or VLANs in the path? Is the Play:3 the affected Sonos zone?