When you make a contra-entry, you pay the same amount off the customer and supplier account. However, if the outstanding invoice values don't match you'll see this message:

'The sales balance does not match the purchase balance - Do you want to make a part-contra for the lowest amount?'

Press Yes

If you press 'Yes', the software posts the contra entries for the lower of the two amounts. You can then pay off the balance of the relevant invoice separately.

Press No

If you press 'No', you return to the 'Contra Entries' window. You can then double check the selected transactions.

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