You need to geta copy of that return to the IRS. At this point in time, you need to print the return, sign it, and mail it to the IRS. Whatever happened to your electronically filed return is not going to matter. What is important is that the IRS gets the correct return.
When you mail the return, use a service that notifies you when the return is delivered. Sometimes the IRS seems to lose returns and all we can do is send it again.