By default, ConnectStock takes the stock for every FBA shipment from 1 warehouse: the store's Local Warehouse. If you also ship to FBA from other places, like AWD or a 2nd warehouse, set the right source warehouse on those shipments.
Change it on 1 shipment (easiest)
Go to ConnectStock, then FBA Shipments.
Click the 3 dots on the shipment and choose "Set Source Warehouse".
Pick the Source Warehouse the units really came from.
Click Save.
Pick the source on each shipment yourself
Go to Stores & Files, then Inventory Files, and click your inventory file.
Click Edit, then Inventory & Warehouse.
Turn on FBA Shipment Source Warehouse. Now you pick the warehouse for each FBA shipment.
Optional: turn on "Auto-Match by Name". If the warehouse name in Amazon matches a warehouse in ConnectBooks, it's used for you.
Click Save.
Shipments with no source warehouse are not transferred. On FBA Shipments they show Missing Warehouse. Click Resolve, or use Set Source Warehouse, to pick one.
Change it on the transfers (another way)
Each FBA shipment makes at least 2 transfers for each item:
From your local warehouse to In Transit.
From In Transit to FBA.
Only the 1st one needs the right source warehouse.
Go to ConnectStock, then Warehouse Transfers, and open the Shipment Transfers tab.
Search for the Shipment ID.
Each item in the shipment shows as its own line. Tick every line that goes from your local warehouse to In Transit.
Click Action at the bottom of the page, then Edit Warehouse.
In Source Warehouse, pick the warehouse the items really shipped from. Leave Destination Warehouse as it is.
Click Save.
Frequently asked questions
Do I need to change the In Transit to FBA transfer?
No. Only the transfer from your local warehouse needs the right source.
I don't see Warehouse Transfers.
It shows only when Warehouse Tracking is on in File Settings and your user has the Warehouse Transfers permission.
When is this useful?
When you ship to FBA from more than 1 warehouse, or from AWD. See How to Handle AWD Inventory in ConnectStock.