Hi,
1) You can not collect the cheque from the bank
2) Beneficiary is hold the right to recollect the cheque from the bank and still he can redeposit you r cheque many times until the expiry of the cheque date (normally 6 month valid from the date of cheque)
3)the only way is talk to the beneficiary request him to get the cheque back from bank and give it to you
4) If he did not agree to do so, then you can visit capital police department with copy of the cheque, proof that you have settled this amount with beneficiary, contact details of the beneiciary.
5) if you dont have any proof, it is hard for you and no way to compromise with the beneficiary.
6) it is very serious issue, try to get back your cheque Soon.