I assume you are using BAPI_SALESORDER_CHANGE
You have to use EXTENSIONIN table and enanche the structures
BAPE_VBAP
BAPE_VBAPX
VBAPKOM
VBAPKOMX
For custom fields.
It's an issue already analyzed and explained in the forum, example here
How to use BAPI_SALESORDER_CHANGE to update custom fields in VBAP