A. First, you need to check the order sheet of the case as to whether the Court has passed any interim orders viz., temporary injunction, status quo order over the disputed land or not?
B. You can enter into registered agreement with the builder if there is no any adverse order against you. However, you need to take abundant precautions with respect to the same viz.,
1. Development of the Property shall be commenced only after settlement of the Court case by providing certified copies of the settlement of the case
2. This Agreement shall be cancelled upon failure of the settlement of the Court issue and the Developer shall execute the Cancellation of the Agreement before the Sub Registrar Office.
3. You may fix a time limit to settle the issue and incorporate a clause towards termination of the agreement by itself on failing to obtain decree copy or compromise decree or settlement order copies from the Court.
4. You can incorporate a penalty clause in the event of failure to settle the matter.
5. You should not delivery of the possession of the property until settlement of the Court case and mention like this.......upon settlement of the Court issue that the Developer shall be deemed to have been handover the possession of the land.
6. Try to avoid register the Agreement as you and your land will have been locked the same by registering the property. Hence, General Agreement with sufficient stamp duty is enough. Else you need to keep on calling the developer to cancel the registration to remove from EC document if the deal is cancelled.