Flat deviation

3 months ago i have booked a 2 BHK flat on 4th floor by providing 20% of total value and made a sell agreement. I have decided to pay 60% of the total value by myself and the rest 40% will be bank home loan. Building construction is almost (90%) done. I was about to take the handover of the flat on April, 2015. Now at this stage the builder is saying that the building plan has been approved till 3rd floor (fully approved) & 4th floor (50% approved) by the municipality. For which my flat has not been approved completely. A part of my flat near about 50% (balcony & a room of that flat) has not been approved. Municipality has penalized a certain amount of money to the builder. In this condition if the builder is paying that penalized amount, will the municipality re-approve the building plan? And after that by using the re-approved building plan can i apply for the bank home loan again & would that flat be completely approved by the municipality (along with balcony & a room of that flat)? I will be great full if you can give me the answers suggest me the correct procedure.