1. Why do you decide about giving three cheques to their proportionate share in the property.
The sellers have to decide about getting one cheque or three cheques in the names of the individuals.
If the son has already given GPA to his mother for the same property, then he cannot give a fresh GPA to another person i.e., his sister without cancelling the existing GPA.
In that circumstances after cancelling the existing GPA, his sister shall be signing the registered sale deed on her behalf and on behalf of her principal i.e., her brother, if so, you may have to draw two cheques only, one in the name of mother and the other on behalf of the sister.
You cannot decide about making the payment to them, you may discuss with them and arrange for the disbursal/payment of the sale consideration amount accordingly, without making anything complicated due to your own ideas.
2. The TDS in respect of the share of sale consideration amount to be disbursed to the NRIs/foreign citizen is to be made by the buyer as per law in vogue, he cannot show any consideration towards their plea on this.
3. If at all they claim any exemption, let them file the income tax returns and claim refund.
If they are ready to produce any certificate to that effect, you may verify the authenticity of the same and consult an auditor before exempting them from the proposed TDS.