The "Are you there" timeout messages still occurs after the bot application has ended the conversation. I tracked it down to this statement in timeout.js
if (event.type === endOfConversation) { **_this.clearTimeoutHandlers(event);** _this.timeoutStore.removeConvoFromStore(convoId); }
actually should be
if (event.type === endOfConversation) { **_this.clearTimeoutHandlers(convoId);** _this.timeoutStore.removeConvoFromStore(convoId); }