Welcome to the forum. The BOM will typically show the part that was used in the assembly. With that in mind I have to ask: "Are you sure that the assembly is referencing the original part and not the new one?" Also, what method did you use to "make a part from another part"?
If I have a part made from another part, I typically do it by inserting the original part into an assembly and then adding assembly features to achieve the modification. Then this "assembly" would be used in the upper assembly. With this method, if you wanted the original part to show up in the top assembly then you could set the configuration BOM options for the modification assy to promote children.