It is possible for 2 invoices to be linked to one progress claim in the Accounting System which occurs via the job number tracking category.
In the most common situation, an invoice can be sent from Buildlogic with a credit note applied and the second will just be a credit note itself - this will cause a doubling of payments in Buildlogic with the credit note.
To fix this error the job number that was applied to the credit note in the Accounting System has to be removed and then the sync needs to be run. From here, remove the progress claim links and re-link.