Income tax refund not received

Dear Experts, I need your valuable advise on an issue I am facing since AY 2016-17. I had filed my ITR for AY 2016-17 after due date but before 31 March 2017. I had claimed certain amount of refund in the same. Thereafter I received some notice from the department asking me to either file the response on their queries related to mismatch of income as claimed by me and as reflected in 26AS or submit a revised return. I submitted my response but they raised same query again, so I filed a revised return. But I have not received the refund till date. As per the status on the website, original return is being shown as invalidated while revised return is being shown as processed. My refunds of later years have been paid by them. When I submitted a grievance regarding this issue, then the department replied that since the original return was filed after due date, it got invalidated. Kindly guide me as to how can I receive my refund. Thank you