The IRS will not remove the indicator that your SS number has already been received on a tax return, regardless of having an amended return filed.
You will have to print and mail your tax return.
See this TurboTax support FAQ for how to print a tax return for mailing when using the online editions - https://ttlc.intuit.com/turbotax-support/en-us/help-article/printers-printing/print-mail-return-turb...
