A person purchases a flat and pays 100% of the flat's value including all other formalities. In return, the builder provides possession but not the registry.
What's next? The Buyer is not interested in money but registry.
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In the US (and, as this is an old Common Law concept, the UK), a court can order "specific performance" (also sometimes called "replevin"), where a party can be compelled to perform specified actions, generally to the completion of a contract. Since you have completed your end of the contract, and they are apparently refusing to do their end, you may have a lawsuit for breach-of-contract.
Since British Law has some influence on Indian Law, this remedy may be available to you.
One complication that I see, is that their ability to transfer the registration to you may be blocked by insolvency/bankruptcy, if the registration has value and if they have unpaid creditors.
I would recommend talking to an Indian lawyer concerning a breach-of-contract lawsuit (and mention to them that your goal is to obtain the registration, rather than monetary compensation), and to explore your options.