Article 138 of NI act

Please be assured nothing will happen. The point is when you have given stop payment instructions to your bank, if you have enough funds in your account to pass the chequ in qustion, such stop payment cannot be considered under Section 138 at all.  Underlying principle is that a debtor should not give stop payment instructions (when he does not have sufficient funds) to escape from being penalised under section 138, Courts will see this fact.

Finally, do you think a school/college will proceed against you under Section 138 (where they have to file a police complaint etc.) for recovery of their fee which may be a few thousands. Its a long shot. Even if they take such foolish step, you are inthe clear as per the law.

Just issue a Registered notice stating that you are not interested in admitting your child in their school, and this was stated earlier also asking school not to present the cheque.  Now that cheque is lying with them, that may be immediately returned to the drawer as expeditiously as possible.