As it appears your question is not about jurisdiction of court. It is about whether the police can arrest you. In other words whether the bouncing of your cheque was a civil case or a criminal case.
The civil part of the case whether you owe the payee the amount of the cheque. Bouncing of the cheque is a criminal offence because Section 138 prescribes a prison term for such an offence. But there is a rider intended to protect you.
The rider is that the aggrieved party has to make a demand for payment of the amount after the cheque has bounced and the amount should remain unpaid for 15 days from the date of such demand.
Did the party serve notice on you? If so how did you respond? Of course it is obvious that you have not paid the amount so far. But did you at least reply and give reason for non-payment?
Notwithstanding any Act bouncing of a cheque is a crime only when there is a criminal intention on the issue of a dud cheque. If there was no criminal intention the burden of proof that there was no criminal intention will fall squarely on the accused only.
If the aggrieved party had sent you a demand notice as required under Section 138 you should have not only explained the circumstances under which the cheque bounced but also have taken anticipatory bail against possible arrest.
It is usual for banks and financing institutions to collect post-dated cheques for repayment of the loans advanced by them and the interest thereon in installments. Criminal intention behind the issue of such post-dated cheques cannot be presumed. Financing Institutions do not advance unsecured loans. There would be hypothecations, collaterals, sureties and also detailed agreements to cover defaults and the bouncing of one of the post-dated cheques alone cannot be looked at in isolation under Section 138.
Yours could be a case of issuing post-dated cheques in good faith but being overtaken by unforeseen events. You say that your firm was forcibly declared an NPA by Union Bank. Does that mean that your cheque may bounce was known to you at the time of issuing them?
In any case only a court can decide whether the criminal part of NI-138 can apply to your case or not. You must have applied for anticipatory bail. If not you may get bail after arrest. You engage a good lawyer.