You need to get the same registered through his legal heirs 

You have to registered sale deed to get the ownership of the flat as per registration act and transfer of property act.

If they are not traceable than apply civil suit in the court for adverse possession and get the order from court that title of ownership belongs to you. And you're real owner.

Registration has to be done within maximum period of 8 months 

your remedy is to ask legal heirs of seller to execute deed of confirmation 

it should be stamped and registered 

Engage a detective agency to trace out legal heirs 

The legal heirs of the seller have to be approached for getting the sale deed executed in your name.

You may issue legal notice to them and demand them to execute sale deed and register it on your name.

You have to trace them out or you issue legal notice to their last known address and get it returned undelivered after which you can approach court to get the sale deed registered by filing a suit under specific relief act.

Then approach court for declaration of the same 

you will have to file a suit against the unknown legal heirs of the seller

in that suit you will seek the relief of specific performance of contract and a direction to the LH of the seller to come forward for registration of the sale deed

if the LHs after issuance of public notice in local newspapers do not come forward then the suit will proceed ex-parte against them and the court will pass an ex-parte decree in your favour

as an alternate relief you have to seek a relief that if the LHs do not come forward for registration of the sale deed then the Court should appoint an officer who would complete the registration formalities on behalf of the LHs of seller/defendants/judgment debtors

in this way the final sale deed will be registered

you will have to pay the full stamp duty again on the sale deed at the prevalent market value minus the stamp duty already paid on the agreement for sale. 

the agreement for sale which is stamped under the amnesty scheme cannot now be registered because a document can be registered only within 8 months of its signing as per the Registration Act 

Dear client In cases where the previous owner/s have passed away, you may contact their legal heirs to rectify the issue. However, if you cannot find the legal heir, a rectification deed without a seller is possible with supporting documents as asked by the sub-registrar.

Respected Sir,

You may file a suit for specific performance.

- As per Supreme court Judgment, provisions on adverse possession are made under the Limitation Act, 1963. In case an owner does not stake his claim over his property for 12 years, a squatter can acquire legal rights over the property.  The prescribed period in case of for government-owned properties is 30 years.

- Since, even the legal heirs are traceless , then the registrar will not register the property in your name. in the absence of the executor. 

- However, as the said property is in your use and occupation for the last 30 years , then you can file a declaration suit before the court on the ground of adverse possession for declaring the legal owner of the property