Based on my experience on my previous partnership visa application and by reading from these forums, as long as the separation is valid and beyond your control like employment, family emergency, etc. INZ could classify you as living together IF you have maintained constant communication while you were away from one another. IF you're able to provide proofs of the 12 months living together requirement they will issue you 24 months visa duration but if it's less than this then they will issue 12 months visa. You have to satisfy the INZ Officer that you are in a genuine and stable relationship by putting forward a strong evidence of this. GOOD LUCK!
-This is not an Immigration Advice as I am not Licensed, this is based on my previous applications, bear in mind that every case is different-