Dear Sir,
It is a bit diificult to interpret your question as you have provided insufficient information and the information provided is again not clear. But still considering what you have said i will try resolving your query.
1. You have said that your brother wants the difference between the HRA and perquisite of Rent free accomodation.
I assume his CTC would have reduced by the differential amount, then he will have to re-negotiate the terms with his employer for the same.
2. Perquisite should not be taxable in his hand - That is again not possible as per Income Tax Act, as rent free accomodation provided by employer is taxable in the hands of employee under the head perquisite.
3. Should pay full HRA and perquisite value may be added in his income - I assume by this you mean he should get full deduction as per HRA and then add back perquisite.
This cannot be done unless the terms are negotiated with the employer - you cannot claim both HRA and Perquisite. He should renegotiate with his employer that he wants to leave the company provided accomodation and move into his own rented/owned premises as the case may be and be given HRA benefits if that leaves him with higher surplus income.