This was copied from help, referring to reference parts.
"Reference Components are components that are used for construction geometry or add context to a design.
Examples of Reference Components are:
Construction elements such as a skeleton part or assembly for skeleton modeling.
Visual enhancements, such as a tote filled with parts sitting on a desk, where the tote is added for technical drawing/publication purposes. It is not a part of the actual design.
When a component has a BOM Structure of Reference, the BOM treats the component and all its direct and indirect children as if they do not exist. All components, that are a part of a Reference component, are excluded from quantity, mass, or volume calculations, regardless of their own BOM Structure value. Reference components also have special treatment in drawing views."
So my question is Do you actually need those construction parts in the BOM?
If you really think that you need them for the export then you will have to change them one by one, you can speed this up a bit but using the drop downs in the "Bill of Materials" command in the assembly file, you can find this in the manage tab.
Keep in mind that if the original designer wanted to use these parts in the BOM then they wouldn't have made them reference.
Good luck!
Ryan
Please mark this response as "Accept as Solution" if it answers your question.