The existence of the owner link between CAD 12345.prt and it's described part 12345 in isolation are not enough to guarantee that part 12345 appears in the product structure. It also must be a member of the parent part assembly.
Check that the parent assembly of CAD 12345 also has a "owner" link to a described part.
If owner link to the parent assembly is present, then try to rebuild the parent part structure. You can do this in the structure compare window, but I think you have to select "edit in a workspace" when setting up the compare. Doing this or simply iterating the parent assembly should bring the part structure back in sync with the CAD structure.
If there is another type of link to the parent part then it means the structure was defined manually and the members could be completely different to those of the describing CAD model.
Darren