hey!.
even if it is not common among indian couples, as long as you have the right proofs which I believe you do by the sounds of it, you should be fine. Common-law is not harder to prove than marriage,just takes more work, its all about the evidence right.
actually for you guys being indian and having the proofs of a common-law relationship, it may help you rather than hinder you, because the arranged marriages which are so common are sometimes harder to prove and require an interview not all the time, but often. so applying as you did may be beneficial.
Everything im reading about your case seems fine, even if you are not together now, it doesnt hinder the common-law application because you did live 12 months together consecutive. alot of common-law couples have to live together than end up being seperate during the process, its not uncommon.
you guys will be fine.