Taking payments outside of the GoCardless for Xero dashboard can lead to a negative balance on the reconciliation account. For example, if you are using a payment plan to take an invoice in multiple payments, the GoCardless for Xero dashboard will not be aware which payments are for which invoice. In this case, we will not be able to push the payment to your reconciliation account, however the full payout amount will be transferred from the reconciliation account to your current account.
To resolve this, when applying the payment to the invoice, you must ensure it is posted into the Direct Debit account in order to provide the full balance for the payout transfer. You must also ensure you mark the payment as reconciled.