Combining duplicate SKUs on a CSV Output?

Hey All,

We use Shipworks with Magento and Magento has a history of sometimes, for whatever reason, breaking up the same sku into 2 different lines on some orders.  I use Shipworks to generate a simple template that outputs ordernumber, sku, qty to a csv file. 

The result also outputs the same sku on multiple lines for the same order if Magento decides to do this. 

Would I be able to have Shipworks detect lines with the same ordernumber + sku, add them together and output as 1 line item?

Thank you

Rob