Yes , amalgamation of 2 Flats is Permissible subject to Pakring and other Requirements, As per Latest Ease of doing Business Circular BMC has brought in a Circular in august 2016 wherein on submission of requisite Docuemnts the permission should be granted in a Day Theoritically but it has become easier and faster for sure.
There is nothing like proper OC (Occupation certificate), building is either with OC or without it. If the building is without OC then fungible Compensatory FSI available on rehabilitation component shall not be granted without charging premium.