Hindus got married under special marriage act how to register marriage

I married under Special Marriage Act on 10th April in Pune Marriage registrar office. I live in Germany currently but hold Indian passport and my perm residence is Pune. My wife comes from Nagpur and was living 6 months before marriage in Mumbai. We applied for german spouse visa at german consulate mumbai but got rejected. They said that our marriage is invalid since we did not reside in Pune 30 days before notice of marriage (Section 5). Even though an Indian authority said my marriage is valid, German consulate is saying it is invalid. We also did traditional hindu marriage in June in Nagpur before decision from Consulate came. I wanted to know whether we could register that marriage under Hindu Marriage Act in Nagpur Muncipal corporation? I need urgent help. Both of us are hindus.