Re register a marriage in special marriage act

Hi, I am an Indian Hindu boy who got married to a Filipino Christian girl in 2015 in delhi in a Arya samaj mandir and then register our marriage in Ghaziabad court under Hindu Marriage act (we follow our lawyer as we have no knowledge about any law). We report our marriage in Philippines embassy Delhi also with the same marriage certificate and they also accepted it and now we are legally married in Philippines also. She goes back to Philippines that time and when she came back to India again in 2016 Indian embassy in Philippines issued her a multi entry spouse visa. This time she was planning to live in India for more than 6 months so we visited the FRO Delhi and they refused to accept this marriage certificate and asked us to re register our marriage under special marriage act. We met many lawyers that time but no one could give us any solution because everyone asked for her single status certificate from Philippines that we were unable to provide because we were married to each other for Philippines govt. While we were knocking many door to get our marriage certificate under SMA we both got the job in UAE And left India before completion of her six month in India. Since then we are living in UAE but next year we are planning to move to India and know that we will be asked for same documents again. So please if you can guide us how to get SMA marriage certificate or what should we do now so we both can live in India for rest of our life without facing any legal issues. We bot will be grateful. Thank you very much.