There are several reasons why QuickBooks might make changes to your previously reconciled cheque payment, Accsys.

The changes could be due to System Administration activities in QuickBooks, which happen automatically when:

• Changes to one record can affect another. (e.g., if a payment is edited and linked to a different invoice or expense account, QuickBooks updates the original records automatically).
• Connecting apps to QuickBooks can result in alterations. When these apps send or modify data in QuickBooks, it appears as a System Administration event.
• Creating recurring transactions, such as recurring expenses, triggers System Administration events once QuickBooks processes these automatically.
• Setting up automatic events, such as bank feed updates, can create System Administration events even when not actively logged in.

Check out this article for more details: Use the audit log in QuickBooks Online.

Since the cheque payment has already been reconciled, I recommend reaching out with an accounting professional for detailed guidance on how to handle and address the changes effectively. This will help ensure your books remain accurate and properly recorded.

Feel free to return to this thread if you have follow-up questions.