Hi Jeano,
Thank you for your post.
I completely understand your concern about the absence of a specific setting for duplicate check number warnings in MYOB Business Lite. If you're referring to this set-up from AccountRight:

Currently, the ability to view or edit reference numbers when recording payments for purchases, as well as the duplicate check warning feature, is available in AccountRight but not in Business Lite.

Our developers are consistently working on enhancing MYOB Business Lite, bringing in features that align with AccountRight functionalities. I'd recommend posting this suggestion on our Product ideas board. Your feedback helps our team prioritize features for future updates.
Please feel free to let me know if you have further questions or any concerns in the future. I'm happy to help.
Cheers,
Princess