It sounds like you are already in the midst of negotiating with the claims department of the insurance company. You should contact the claims representative you have been dealing with and let them know about the issue with the title. Likely the difficulty with the title will probably just hold up the settlement of your claim until you have the duplicate title in hand. If you need the settlement sooner see if there is any rush fee you can pay to the state for the title to be processed faster.
Stand Up and Settle Your Insurance Claim is an article in our Learning Center that can help you get through your negotiation process.