Leave and licence agreement was only for period of 12 months 

2) period of leave and licence has expired 

3) if registrar is insisting on presence of both parties and license refuses to cooperate issue legal notice to licensee to appear before registrar office on x date for removal from EC 

It automatically gets expired you don’t have to cancel it after expiry period 

You may issue a notice to the tenant to co-operate for cancellation of registration, failing which you may attach the copy of the notice and submit a cancellation deed unilaterally to the sub registrar. 

Records are required to be rectified accordingly. Registrar is acting in routine manner without application of mind. In terms of law  the rent agreement automatically got cancelled and terminated and nonest by aflux of time after expiration of 12 months and that too when the same was neither extended nor was renewed. File application for rectification of record and if record is not rectified then lodge complaint on portal and if need arise file suit for mandatory injunction against registrar and state govt. Take help of a competent lawyer. 

- Since, this leave and license agreement was executed for 12 months only , then after lapsing of this period , the agreement has lost its validity. 

- Further, as per Registration Act, a notice to the other party is necessary for the cancellation of any deed. 

- Hence, you can send a notice to the said tenant for the  execution of cancellation deed and to appear before the Registrar  or to issue an NOC

- Further , if he will not appear before the registrar office , then you can submit that notice for removing the status in the EC. 

Here are a few steps you could consider:

Consult a lawyer: Given the complexity of your situation, it's advisable to consult a lawyer who specializes in property and tenancy law. They can provide you with specific advice based on the laws and regulations of your jurisdiction.

Communicate with the tenant: Try to reach out to the tenant and explain the situation to them. Express the need to remove the entry from the Encumbrance Certificate (EC) and discuss the possibility of their cooperation. You may need to negotiate with them and potentially offer an incentive to encourage their cooperation.

Serve a legal notice: If the tenant is uncooperative, you may need to serve them a legal notice requesting their presence for the cancellation of the agreement. Your lawyer can help you draft and serve this notice according to the relevant legal procedures.

File a petition: If the tenant still refuses to cooperate, you may need to file a petition in a civil court to seek the cancellation of the agreement. Your lawyer can guide you through the necessary steps and represent you in court.

Seek a court order: If the court finds in your favor, it can issue an order directing the registrar to remove the entry from the EC. This court order will then need to be submitted to the registrar's office for compliance.

Disclose the situation to the potential buyer: It's important to be transparent with the potential buyer about the situation and inform them that you are actively working to resolve the issue. Depending on the buyer's preferences and the legal requirements in your jurisdiction, you may need to provide suitable assurances or documentation to address their concerns.

after 12 months, agreement expired. Any document register at Registrar will always reflect on records. 

Registrar is fooling you to execute cancellation deed of document which is already expired. 

Rent agreement will always reflect in EC. New change will be next registration that will be cancellation deed which will have no effect.

You can give application to the concerned Registrar and if no action is taken/ rejected then you have to send legal notice to him to remove the entries. If he fails to comply it then you have to file suit calling upon him to remove that entry from the EC