When Link-Attributes are used in the Product Structure like usage attribute "Line number" or Occurrence Attribute "Reference Designator" - they are always related to the next parent object.
Therefore - a "Line number" or a "Reference Designator" is always the same when the assembly will be reused.
But sometimes it is necessary that these attributes are related to the top-object of the BOM (eg: End Item).
As a result, an attribute value can be different depending on the assembly situation.
Siemens Teamcenter for example can deal with this situation pretty good. As a result, we have a challenge here in projects where we have to replace TeamCenter with Windchill.
It seems that there are first drafts in the Windchill Database for this kind of solution - as there are tables called: "PARTPATHOCCURENCE", "PATHOCCURENCEUSERIBA",...
Maybe it can also be managed using BOM-Transformer and Equivalent Occurrence enhancements.