In a cheque bouncing case, there is a possibility for settlement out of court. When a criminal complaint is filed for a cheque bouncing case, the law allows for settlement. This is done through a legal concept called compounding of offences.
In this process, the payee/holder of the cheque agrees to not file a court case or agrees to withdraw his court case in exchange for some compensation (usually monetary).
This can happen at any stage of the court proceedings.
The law allows such an agreement to reduce litigation and burden on courts.