Note that while OrderTotalCalculationService does handle the shipping 'total' by making adjustments, such as free shipping, discounts, tax, etc, it's the shipping rate provider plugins that determine the base shipping rate.
The pdf invoice shipping rate is not "calculated". The order already has that information recorded, so it just displays what's on the order record.
RE: "same amount sent for payment as well?" Shipping is included in the "Total" (as is tax). There may be an additional 'payment fee'.
What have you changed ? If you changed a plugin then install the new version of the plugin on your production server using Admin If you changed the core then copy the new .dll to the production server then restart the webserver
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