A. Have you got the registration Sale Deed or Agreement for Sale?
B. You need to get the NOC from the builder and you can enter into a Deed of Exchange and you have bounden duty to pay the additional amount in respect of 3 BHK.
C. Moreover, if you got the registration of Sale Deed, you have another option also, you can release the flat to the builder by execution of Release Deed by receiving your total consideration amount. Later, you can enter a fresh Sale agreement for 3 BHK.
D. In my opinion, Deed of Exchange of flat is more better. Contact local advocate for additional query and draft of your deed.