When building a parts list, you create a list of parts for a given system type, and assign them the desired styles. Rules are never run automatically, only at creation time and when the Apply Rules command is run. You can apply rules by selecting a pipe or structure in a drawing, then right-click and click Apply Rules. This is designed so that undesired changes are not made automatically, or accidentally; you must actively run them.
You can bulk edit part list rules and styles in the Panorama view. Right-click on the column header and select Edit.