Can you call Immigration telling them you have been waiting for the ref no and ask them to check for you. Then, you will know whether Immigration has recieved your application. Try 2111 8435.
It shouldn't take that long. If the agent said the application was submitted in mid Oct, you should get the ref no by end of Oct, even you missed some documents. It usually takes a week for HK Immigration to provide the ref no. Have you called and asked HK Immigration why you still not yet have.
Is the agent really submitted the application? Any proof from the agent? I am afraid the agent didn't and told you that your helper does not want to com. When you run out of time and are about to give delivery, you will end up taking anyone available from the agent as the last resort.
I am very upset with some of the agents in the way they run their business.