base on what i know, when a P3D object is selected, center lines of connected line to it(or lines with the same line number) whether those lines are hidden will appear, try selecting a single piece of component then use add to selection, all connected parts or all line numbers, hopefully it would help you troubleshoot your model. thanks
Best Regards,
Pat Andres
Autodesk Expert Elite
Plant 3D Administrator
GHD Manila