I can not speak for BTCPay but I know that there was some debugging going on in regards to how BTCPay subscribes to events.

To answer the question about the relay:
if the Alby relay is going away you just use a different relay. in that case you will have to reconnect the app (btcpay) to the wallet that you use again. (because the relay is set as part of the connection secret and the app and wallet need to know through which relay they have to communicate)
but that’s the beauty of NWC, it uses the default Nostr infrastructure and no special setup would be needed in that case.