Marriage anullment for marriage under Special Marriage act

Hi All, I wanted to seek an expert advice on procedure for getting marriage annulled under special marriage act. We got married in church with all the proper ceremony 10 days prior to getting married again under special marriage act in kerala. Instead of getting the marriage registered we married under special marriage act. This was a mistake that was done on our end. She has returned back to Germany and I have applied for the family re-unioin visa. Since we heard from other people that church marriage was not considered in case of family re-union that was the reason for getting the marriage done under the special marriage act in first place. I submitted both the marriage certificate and the certificate under special marriage act, Embassy suggested me to cancel the former since it was unnecessary and they do accept Church marriage. They pointed out that the marriage is void since we both were married to each other earlier in church 10 days prior. I wanted to know about the procedure to go by and if there would be any complications. Thanks