Hi Basketball,
Thank you for your post and your patience in waiting for a response.
Regarding your concern about the deselected lines in the Prepare Electronic Payments screen, you don't need to worry about reconciliation issues.
To clear the reversal (negative amount) and original payment from the Prepare Electronic Payments window, go to the Prepare Electronic Payments window and select the negative and positive amounts (which should give a total of $0). Click on the bank file. Click OK in the window about recording the negative transaction. Then cancel the window asking you to save the bank file.
Our Help article, Making Electronic Payments, has detailed information to assist with this.
Feel free to create a new post again if you require further assistance.
If my response has answered your inquiry, please click "Accept as Solution" to help other users find this information.
Cheers,
Princess
