A Rejection Notice will remain on the main page of the tax return and also in client status until you receive an 'Acceptance Acknowledgement' from the IRS. When the accepted status is received, the program will automatically remove the rejection notice from the return.
Mailing a paper copy of a rejected return will not generate any acknowledgements, and therefore will always show as a rejected return. In order to help keep track of returns that you have mailed in already, consider adding return notes. To display instructions for entering return notes in the tax program click here for step by step instructions.