I received another CP59 notice after I filed my late taxes for the same year. My account for the tax year has code 599 indicating the return was received by the irs. Do I need to send the return again

No, do not send the return again. Just reply to the letter that you have filed the return and the transcript shows a code 599 which means as you understand it that the IRS has received the return. Then let them figure it out.