1. Why was the builder buyer agreement prepared after the allotment of flat?
2. A co-applicant is a person who applies along with the borrower for a loan. A co-applicant becomes equally liable for repayment of the loan amount in case of default by the primary applicant.
3. Your wife must have been a co-applicant only at the time of applying for loan to LICHFCL. Nobody could have been inducted as a co-applicant in the agreement you entered into with the builder. If you alone have signed the agreement as a buyer then the builder is liable to register the conveyance deed in only your favour. Your wife cannot legally insist that she should also be made a co-owner by virtue of being a co-applicant for loan.
4. If builder is not cooperating then issue a lawyer's notice to him for cancellation of the agreement and/or to claim the refund of advance and damages.