First of all you need to tell that is it a bailable warrant or non-bailable warrant in either case you have to appear before the Ld. Magistrate and file an application for cancellation of warrant with explanation for non-appearance on date fixed. Non-compliance of order may lead to proceedings for proclamation. In criminal cases it is advised to not jump the order of court if you are unable to appear before the court instruct your lawyer/counsel so that he can file exemption application. You may apply for permanent exemption at latter stage but first of all you need to get the warrant cancelled. Detailed advise can be given only after perusal of record/ warrant. Amount of cheque is immaterial for cancellationof warrant.
Your Advocate need to appear before the court with proper application of cancellation of NBW's. Make sure you don't appear because they will put you under arrest. if you have any proper medical condition then, that can be made a ground for cancellation of NBW's.