FBA & FBM orders are reflected on the dashboard, however the shipping cost for the FBM is only reflected the payout reports. Merchant fulfilled orders are excluded since they can be created for a variety of reasons and would cause duplicates if they were included.
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Merchant fulfilled orders are excluded from the Dashboards, but not from Orders List or Payout Reports. You shouldn't need to calculate these costs manually because the numbers are calculated automatically for you on the Orders List, and also taken into consideration in your Payout Reports as well.