Hi
At the outset, i wish to state that the indemnity bond provided by the Seller quoting the registration sale deed number is Perfectly OK and hence there is no cause of immediate worry.
Should there be any problem in future , you can add 2 witnesses of your choice at a later date in the same indemnity bond.
Next steps ( being 200% cautious) :
1) Since it is a cheque issued by the bank( on account of a loan) you can ask the bank to inform you once the cheque has been encashed by the seller and take a bank statement to that effect so that you are in possession of proof that the cheque has been encashed by the seller and the cheque was issued on your behalf by your bank from your loan amount sanctioned.
2) You can also ask the seller to issue a receipt for the cheque amount acknowledging that he has received the Full payment of the sale consideration and hence there are no dues from you/ your bank on behalf of you.
Hope this helps.