1) Ask builder to give compensation accordingly to property share of that particular owner. This can be tackled at builders point of view because builder has earned lots of money by selling the flats.

1. It appears that you have made the full payment and only physical possession if left to be handed over or it is already done.

2. Since the constructions is almost done the litigation would not pose much disturbance.

3. If the defect remains then you can file case before the consumer forum claiming damages and compensation. 

You can take an indemnity bond from builder that he will indemnify from all the losses.

The seller is bound to disclose to the buyer any material defects in the property or in the seller's title thereto of which the seller is and the buyer is not, aware and which the buyer could not with ordinary care discover.

Any omission to make such disclosure is fraudulent.

In this case the original seller would be held liable and can be sued for fraudulently selling of the property under criminal law. A police complaint/FIR against the seller may be lodged in local police station. 

Further the seller can be sued in civil court for recovery of the consideration amount paid by the buldder and flat owners and for claming appropriate amount of compensation for damages, irreparable loss and injury and mental agony caused due to above.

The builder is bound to indemnify the flat owners as per the indemnity clause in sale deed in case of any third party claims 

The ongoing court case was not in your knowledge when you purchased the flat and took loan on it. Therefore it is a case of fraud and criminal breach of trust and therefore file a fir against him. Also demand full payment along with interest from him by filing a complaint against him in the district consumer protection forum.

Regards 

You can demand indemnity bound from builder.

See you after formation of the association can join as the necessary party in the suit or an intervener to observe and keep track of the proceedings. Further on hand over agreement it can be mentioned any litigation cost and litigation before handover date shall be responsibility of the builder.

1. the flat which you have purchased will not be affected by the ongoing case

2. the claimant's claim is on the land 

3. the builder was liable and obligated to disclose this fact to the flat buyers 

4. the community/society of flat purchasers should intervene in the pending case and seek its impleadment as a defendant party as the society has now got valuable rights over the land over which the case is ongoing. Also the plaintiff party who filed the case must be aware of the construction being made on the land by the builder and must also be aware that the flat purchasers will form a society. As the outcome of the pending suit will have a bearing on the society's right over the land, the society needs to intervene in that suit and file its say 

5. at time of conveyance by builder to society, the society can also take a covenant from the builder in the conveyance deed itself that he undertakes to indemnify the society in case the land sought to be conveyed by him to society is adversely affected by the final outcome in the pending litigation which was not disclosed by him to the flat buyers

6. the flat buyers and the mortgagee banks can also independently file a suit against the builder for non disclosure of this important and vital information and keeping all in the dark and thus damages can be claimed from the builder

7. its really a complicated situation. The mortgagee banks and the flat buyers would also to some extent be held accountable for not having exercised due diligence before sanctioning loans/buying the property 

As far  as you the buyers of the flat is concerned you need not worry since your buying is genuine and also the legal opinion through bank is also perfect.

You may just wait and watch the outcome of the pending litigation.