Amazon recommends that no one uses 3rd party apps for sending FBA inventory to the warehouses.
Please create a transfer option that reduces inventory en masse.
Your support people have told me to download the inventory and then subtract what I have sent and then upload the inventory again.
That is tedious and doesn't always work.
The other way I have been told to do it is to select each SKU individually and then manually change the inventory with the add (-) to the on hand.