Company has already filed a case U/s 138 as the OP says.
s. 138 says :
138 Dishonour of cheque for insufficiency, etc., of funds in the account. —Where any cheque drawn by a person on an account maintained by him with a banker for payment of any amount of money to another person from out of that account for the discharge, in whole or in part, of any debt or other liability, is returned by the bank unpaid, either because of the amount of money standing to the credit of that account is insufficient to honour the cheque or that it exceeds the amount arranged to be paid from that account by an agreement made with that bank, such person shall be deemed to have committed an offence and shall, without prejudice to any other provisions of this Act, be punished with imprisonment for a term which may be extended to two years or with fine which may extend to twice the amount of the cheque, or with both
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It is now for the Court to decide how sound your case is and what penalties to impose. You would have got a Notice from the Company earlier demanding payment and now that a case has been filed a Notice/Summons from the Court also , enclosing the Written Statement of the Company which should set out clearly why they are claiming this amount.
If you can rebut their claims in writing, with strong evidence to back it up rather than just statements you may have a case. Else you have no case, IMHO.
Suggest you take advise of a lawyer now.