Duplicated Sales Order Lines within an order

[FM6]

We have a BOGOF deal.. customer buys 2 of the same SKU and then a 3rd same SKU is added to the order as the free item.. 

here is the problem.. 

The order sales lines are added in this way;

2 x SKU 1234

1 x SKU 1234

Is there a way to make the system add it in the correct way like below;

3 x SKU 1234

We have a WMS system that connects to our shopify to download the orders as we use the WMS system as our main system. 

The problematic orders come through to our wms system perfectly fine however when we go to dispatch the order via Royal Mail (click and drop), the order fails to process because RM see the order lines as duplicated. So we have to then edit the order on our WMS (delete the duplicated line and simply change the remaining line quantity to 3). This then allows us to process the order on RM however this then stops our WMS system from marking the order as shipped back on Shopify of course as there is no longer a match on the order.

This is an absolute pain of a problem and the only way round this is to see if the order lines can be merged direct from the source on shopify. Is this possible as surely we can not be the only ones faced with this problem.