In the Shopify Admin, you can mark individual fulfillments or all fulfillments of an order as "In progress".

To only export orders that contain a fulfillment where the status is "In progress", you can add this filter under the Custom Filters section of the Data Settings:

• Fulfillment Orders Status contains in_progress

For orders with multiple fulfillments, you can filter at the line item level as well so only line items part of a fulfillment where the status is "In progress" will be exported using this filter below:

• Lineitem Fulfillment Orders Status contains in_progress