1) is the POA registered 

2) if so on basis of registered POA mother can execute sale deed in her favour 

There are below options:

1. Ask his legal heirship to get succession certificate from court that their father has been dead.
2. If he is missing more than 7 years than file claim by there legal heirs for death certificate and than take succession certificate and later you can proceed with registration of your flat.
3. If the legal heirs are not listening than you can go for adverse possession and file case. On adverse possession court may grant to transfer the flat on your name. As its more than 12 years passed away.

See your mother need to file suit before court seeking direction from court of ownership over the property.

The only way to apply court to issue necessary directions to registrar to register the document in absence of the owner. 

Show all transactions details with the owner and state the fact that owner is not traceable since long time back. 

- A property cannot be registered in the name of buyer , in the absence of last owner.

- Further, a POA holder cannot get registered the same property in his /her name legally.

- Since, your mother having agreement paper, possession certificate , POA, and other documents in her support , then on the baisi of these documents, you should submit a written application for transfer the share certificate in her name , and to transfer the property on behalf of untraced owner. 

- Otherwise, you will have to trace the legal heirs of that last owner for the same.

- If , the society refused for the same, then you should file a suit for decleration before the court , on the basis of documents , and payment proof. 

OPTION-1:

1. Alongwith all the relevant stamp duty paid documents, file affidavit with the local Registrar of Sub-Assurances, to register the Deed. This Deed CANNOT be directly registered on Mother's name.

OPTION-2:

2. IF above is refused, THEN file "declaration suit" in local civil court, for directions to registrar to register the document.

3. AFTER above, Property Deed can be transferred to Mother, with  joint consent of all the legal heirs.

Firstly if the building is on collector land then the collector's permission is needed for the transfer

As the original owner is not traceable the only option now left is to file a suit for declaration in the civil court 

This suit will be filed against the original owner, legal heirs of original owner (because if the original owner is dead and suit is against a dead person, then such suit becomes  bad in law), the administrator general of the court and the society

Prior to filing the suit you can issue public notices in local newspapers calling for Information from public about the previous owner

If no information is received pursuant to the public notice then you can proceed with the suit

The relief will be for a declaration that your mom is owner of the property 

If no one appears for the original owner or the unknown legal heirs of original owner then the administrator general of the court will be directed to conduct an Inquiry and submit a report. 

The court will then direct the AG to register the document on behalf of the original owner, in favour of your mom.

If no one contests the suit it essentially means that it will proceed exparte

A direction can also be sought against the society to recognize your mom as society member after the registration procedure is done in her favour

You first issue a legal notice to the previous owner in this regard and demand for completing the registration formalities.

Let the notice return undelivered.

Then you can approach the society for further course of action in this regard to register the property to your mother's name, if the society do not entertain your application then you may approach court seeking direction to society to register the property to your mother's name for the reasons that you have stated  and based on the supporting documents to your claim in this regard

If it's not transferred from previous owner you need to approach court or the said owner or his legal heirs are not traceable. 

1. Unless the registration takes place the title does not pass to your mother. Consequently your mother has no right to pass the title as she herself is bereft of title to the property.

2. You have to trace either the seller or his legal heirs,

It will register by paying penalty. Apply for it, notice will issue by registrar to seller last known address which must be given on agreement. If he will not appear, sub registrar may registered it in seller absence after charging penalty.

And society demand of cannot transfer the flat till 5yrs was illegal. Society could not have do anything if property transferred anytime. 

1. File an advetisement in newspaper about it. 

2. Try to send a notice to his last known address. 

3. If all fails then file a suit in the court for declaration of property. 

4. Consult a local lawyer in this regard. 

You can use the POA for registration of flat on your mother name. 

If sub registrar refuses for the registration of flat then you can file a declaratory suit for claiming the ownership of flat as per documents available with you and make application for mandatory injunction for registration of flat to sub registrar.

This is my response to you:

1. You have a few options at your disposal;

2. You will have to issue the owner a notice;

3. If he does not, then Registrar has powers to issue notice;

4. If he still does not show up then you will have to approach court under specific relief act;

5. You can also file a suit for declaration of the property;

6. Consult a local lawyer, discuss full facts and take steps.