Cancelled invoice in which WHT is applied

Hi,

As invoice was created and WHT was applied and also a withholding tax invoice was created. But found that the tax code was wrong and discarded the line and has entered another line with correct tax code. For the discarded line a WHT invoice with negative amount was created. But at the time of payment through payment batch, the main invoice, WHT positive invoice's are only appearing in payment. As the negative WHT invoice amount is not appearing, more payment has gone to vendor. How can that negative invoic

Can anyone help on this. Is anything wrong in our process.