Hi,
Your case seems to be a peculiar one. In my experience, banks have allowed the withdrawal of the remaining amount, on submission of the the sale deed of the new property, proof of payment of stamp duty within the two year time limit, and a certificate from a CA instead of an ITO. Further, since your client has sold a residential property and bought another residential property, only the amount of capital gains has to be invested and not the entire sale consideration. Banks have allowed my clients to withdraw the excess money based on the certificate of a CA and had not insisted on a certificate from the ITO.
Regards
CA Keerthiga Padmanabhan
M.Com., CA, LLB