To fulfill a Sales Order on with different line level Locations, customize the Sales Order form and add Location per line item. Below are the steps:
1. Navigate to Customization > Forms > Transaction Forms
2. Click Customize or Edit before the name on the preferred Sales Order form
3. Go to Screen Fields tab > Columns sub tab
4. Mark Show check box for Location then Save.
Setting Location per line item allows multiple Item Fulfillments for different Locations.
Please note however that if Multi-Location Inventory feature is enabled, Item Fulfillment can only be saved from one Location at a time. Thus, after fulfilling the orders on Location A, return to the Sales Order and fulfill other orders on Location B.
Trying to fulfill more than one location at once will result in the below error:
Fulfillments can be shipped from only one location when using Multi-Location Inventory.