OK, I see what you're doing.
I know this is confusing, but the 'Clean-Up' routine that you're attempting to use was never intended to remove Assembly specific edits of the color and translucency made to the actual
Component itself. Rather it's there to remove the edits made to the color and translucency of Component
geometry.
Now you may think that this is just semantics but there is a critical difference between the Component object and the object(s) which makes up a Component.
To start with, you need to understand a couple of things, for one, Components don't really have any display settings (at least not by default), but rather they inherit the appearance of the objects that make up the Component. And second, while we do allow you to perform Assembly specific display edits, they can be applied at two different 'levels'. The first being on the Component itself and the second is on the objects which make up the Component.
Now I have to admit that if you're creating you models using solids and you've not changed the default behavior of Reference Sets, then the majority of your Components, when you access them at the Assembly level, will be made up of only a single object, the model's solid body, but that's not mandatory. So lets take a situation, for what ever reason where you have two bodies in your component, each with a different color. Now when you see this Component at the Assembly level, you will see the two different colors. Now if you were to select the Component object itself, which unless you've changed
Preferences -> Assemblies is the default behavior, both bodies will appear to have changed colors, but actually what you've done is assigned a color to the Component which overrides the color of the bodies. However, if you were careful and used QucikPick (or you changed the selection behavior in
Preferences -> Assemblies), you could have selected one of the bodies and edited it's color, but that would NOT have changed the Component, only the color of a Component object (note that this would still be an Assembly Specific edit, just that it would be applied to a solid body and not the Component).
OK, so here's what I think you've been doing. You've been editing the display of the Component themselves, which is what we expect most people to do, and therefore you have actually edited the 'Properties' of the Component, in this case, you have applied display settings where there were none before. But despite what it might look like, the color of the solid body object inside the component wasn't actually edited and therefore the Part Clean-Up routine had nothing to reset.
Now you may ask, if I don't use Part Clean-Up for this, how do I 'reset' the Assembly specific edits to the display of the Components in your assembly? As mentioned in the last paragraph, what you had done was modify the 'Properties' of the component (that is, giving them a display setting). So to undo that, select all the components in the assembly, or at least the ones you wish to change back to their original appearance, place your cursor over the selected objects, press MB3, select the 'Properties' option and open Assembly tab. If any of the selected Components have any Assembly specific displays edits applied to them, you will see one or more of the three 'Specific...' options toggled ON. Just toggle OFF those that you wish to reset and hit OK.
I know this may appear to be confusing at first, but if you continue to ONLY edit the Component object as it would appear that you're doing now, then continue to use the 'Properties' dialog to reset any changes.
As for why we continue to support the Part Clean-Up routines, they are primarily there to support older legacy workflows some from prior to when people used primarily solid modeling, back when components were often made up of many different objects, including curves, surfaces, etc.
Anyway, I know this is a long reply, but I think it's important to understand what's really happening and why you need to learn the differences in how the system works so that you understand the approaches that you need to take when confronted with something unexpected at least not fully understood.
John R. Baker, P.E.
Product 'Evangelist'
Product Design Solutions
Siemens PLM Software Inc.
Industry Sector
Cypress, CA
To an Engineer, the glass is twice as big as it needs to be.
