Invoices that have positive and negative lines that result in the balance of the invoice being $0.00 are captured differently among accounting systems.
These are sometimes used to Journal an amount from one account to another without creating a manual journal. They are also sometimes used to process a bill to pay for the Activity Statement.
In Xero however, $0.00 Invoices are considered to be paid and this is different to other accounting systems. It is not possible to get the transactions in Xero to reflect the transactions in another accounting system.
This results in a discrepancy between the GST report from another accounting system to Xero.
Transactions that are prior to the conversion date are unlikely to impact the Business Activity Statement. However, they will be recognised on the GST reconciliation report in Xero.
Transactions that occur after the conversion date will create a difference between the Business Activity Statement in another accounting system and Xero.
For additional information in regards to GST differences please see here.