In Sales Order Setup Options, what do you have defined for your "User Shipping Code to Calculate Freight" value?  In a test company, test how changing your setup option to NO works in that same scenario.  However, setting it to NO means you can't add new Ship Via's codes and user can "free form type" in that field.  

Use Shipping Code to Calculate Freight

• Select an option to define how to calculate freight.
• Select Yes to use preset shipping codes to calculate freight charges.
• Select No to manually enter all freight charges, or if freight charges are not required.
• Select Actual to calculate freight charges using the total weight of all items ordered; this option allows you to use ship codes and the actual weights from the Item file and is available only if the Inventory Management module is integrated with Sales Order. Individual shipping codes are defined in Shipping Rate Maintenance.

Set this SO Option to "No" and it should stop Sage programming from resetting typed freight amounts.

To my best knowledge there is no way to configure a Shipping Code for 100% manual freight amounts.

Maybe someone from Sage can clarify how to do that.

Please verify answer if the responses in the post have answered your question.