Not filed means not processed, in this scenario. You are working with the IRS to get your return processed. The IRS is making sure that you are entitled to the refund expected and not someone else.
TurboTax is not informed of the status of your return, once the IRS accepts the return. For Privacy reasons, the IRS does not share that information with TurboTax. All refund inquiries should be made to the IRS in the future as they are resolving an identity issue for you.