Both Shipment Quantity and Amazon Quantity values change over time in Seller Central as you sell FBA items and your FBA shipments are received and processed by Amazon. These values change automatically in Seller Central but they remain unchanged in SellerEngine Plus if you don't download your FBA listings or retrieve your Closed shipments.
Discrepancies between what quantities are available on Amazon through FBA and the Amazon quantity field in the inventory database are caused in time by the fact that SellerEngine Plus does not automatically retrieve updated information from Amazon about your FBA items to then update what you see in the inventory grid.
►Update Amazon Quantity column
You need to periodically download your listings from Amazon if you want to see updated information about quantities available through FBA. To do this click 'Import' > 'Download and Import Amazon-fulfilled inventory (AFN)'.
►Update Shipment Quantity column
As for updating the Shipment Quantity values, in the FBA Shipments Manager tab click the Closed tab, then click the "Retrieve from Amazon (Closed)" shipment button.