NEST Pension opt outs cannot be sent electronically due to refund shown on pension upload report

In Earnie pension refunds did not show on contribution report therefore file uploaded successfully. In Staffology the refund amount is shown as a negative amount which reduces the total amount of contributions due, therefore incorrect. This upload is also failing due to any opted out members are still shown on contribution report and cannot be matched with NEST. there is the option to Tick exclude and employees with no contribution. Should this also include exclude members that have opted out or negative contributions or a separate tick box?

We are a bureau serving over a 1000 clients and monitoring and uploading any opt outs manually is adding considerable processing time.