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Overview

You may get more shipments than required on a sale order, particularly if you are using automatic warehousing. The simple fix for this is to merge the shipments from the sale order (same sales order).
The concept of service orders is that it only has one shipment.
When you merge shipments from service orders, then one of the shipments being merged is deleted.
If the deleted shipment (that is the one you are merging from) is for a service order then there is no way of knowing when that service order is completed and no one of knowing when to remove the inprogress status or what service order was linked to the shipment merged from.

Procedure

If you have two shipments on a sale order and you only want one shipment. Highlight both sale shipments then click on the merge button