Dear Colleague,
The given fact is that you are breaking a bond agreed and ready to compensate as per clause agreed. In future to the maximum extent kindly do not enter into such "bond system" which is mostly used very unfair in our country. Second never deposit your original certificates to any one. If such demands, reject those offers and look for better employment contracts.
Try your best to collect the certificates back and then given Account Payee Cheque etc. Both has to take place simultaneously.
For the present situation, you may send legal notice to them if they are not responding within reasonable time. Sort Legal case if they are still not responding to the legal notice. They will definitely come in line.