Income tax refund

Dear All, I want to discuss with you very unique query. I filed my Income Tax Return of AY 2016-2017 on 6th July 2016. On same day I E-Verified the same. But after few days I realized that my CA considered my wife’s bank account details in it. So I revised the same return with my bank account details. But yesterday my Wife Account got credited with my Income Tax Refund amount. Bow as per section 139(5) revised return replaces original return. But in my case CPC considered my original return only. So whether they will again process my Revised Return? and as a good tax payer of this country, what is my duty in this extra ordinary situation.