Isseud a blank check

1) under law, stop payment does not remove liability. You could also lodge an FIR reporting the cheque as Lost and provide a letter to the bank accordingly. It could be of some help later. In fact, your landlord should file this FIR since the cheque was in his possession and give a copy to you.

2) get all the facts in writing  from the landlord and send them in turn a letter / email reiterating them. If the landlord hesitates you would know his intentions.

Dear Client,

You need not to worry at all, just send a letter to the land lord that he should send back your security cheque as total cost amount of the property is credited in his  account by the Home Loan providing financial institution.

After sending the above letter where in specifically mentioning the words that it was a "security cheque", You can also direct the bank not to clear the cheque as "Stop Payment" instructions.

Here it is to note that at the time of issuing the cheque there should be no liability on your head;  as the cheque should not be issued against any existing liability in other words and the cheque is issued only as a security cheque. The provisions of the Sec 138 NIA does not attracted against any security cheque please note. However he can put a simple recovery case against you or recovery suit under summery trials in civil court on liability grounds, if any..

Yes indeed S. 138 NI Act does not apply to cheques given as Security so solution as suggested is a way out, if not contested by landlord. Since he is already claiming cheque is lost if you can mention that and get his confirmation on that too your case is stronger IMHO.

otherwise, a prima facie case lies under S. 138 when a cheque bounces and decision taken per evidences lead by each party.

It appears you have requested the the return of blank cheque form your landlord only orally and not in writing.  Now, you send a communication to him in writing requesting the return of your duly signed blank cheque held with him for the purposes of security for the release of loan amount due to him and since he same has been fully paid to him, he would return the cheque to you.  You should send the request letter by registered post by retaining a copy with you. There should be a mention that you have already issued instruction to the bankers to   stop honoring the cheque if presented since he had instructed you to inform your banker to stop payment.  With this you can challenge his  case any time in the future if he tries to sue with false case.