Integrate with GoCardless the same way as you work with PayPal
GoCardless integration with KashFlow is great if you are driving the transactions from KashFlow however if GoCardless is creating new customers and generating invoices then the current integration requires significant time to get the invoices, payments and fees into KashFlow.
This would be made easy with a PayPal style integration with GoCardless giving KashFlow a fully integrated solution,
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As you are working on GoCardless integration has your development team thought about this working the other way around where GoCardless drives customer creation and invioces/payments