You might need to restate your question clearer. Are you referring to changing component on a BOM then comparing? It will show that in one iteration a part exists and then in the next, its gone. Reverse is true for added components. Nothing then something. There are options to include part differences.
I would add that if you use the "replace" command in the WTPart structure, the compare will show that the first part number was changed for the second one.
