You can make a single agreement to sell 2 different flats but selling 2 different flats as one is not possible because there will be 2 different revenue records in the municipal based on the plan of the building.
Ask the builder to make a amalgamation of the 2 flats and give one Khata (Revenue record) to show the exact measurement of the flat as one unit.
OC for the flat is must before sale of the flat.