Twitch recently added threaded replies in chat and the bot is updated to reply to said chat messages. To send a reply to a specific chat message you can do x.ReplyToMessage(…) where x is an instance of my Twitch chat lib.
Required
Add as reference: BlushyFace.Twitch.Chat.V2
Example
await client.ReplyToMessageAsync("messageid", "channelname","this is a reply");