If any changes are made to the BOM (i.e. Tax Removed on BOM, Sell Price Adjusted, Quantities Adjusted, Etc.) and the order needs to be re-processed you must re-process in the "Order Entry" module. To do so follow the instructions below:
Highlight all of your lines on the bottom portion of the "Order Entry" screen
Hit "Delete" on your keyboard (you should now see no lines on the lower portion of this module)
Re-"Set" your quote in the "Chosen Quote" drop down
"Process BOM" and "Process"
"Save"
This only corrects the order (customer invoice) so if anything cost related / vendor PO changes were made, adjustments will also need to made in the "View/Modify Purchase Order" module.