It's quite common that a client and builder make changes that deviate from the approved plans during construction.  A new set of plans - Deviation Plans will need to be submitted to your local authority as soon as possible.  Fees will be charged for the new work and you will also have to submit a copy of the previously approved plans together with the new plans to Council.  You will not be able to get an Occupation Certificate without approved plans showing the changes you have made.