If you use Solid Tools to intersect multiple solid groups/components with each other, you may have noticed that when it is used on a component, it's actually replaced by a new group.... Your component is never edited.
So if you're trying to use Solid Tools to make changes to multiple component instances in your model, it won't work. Actually, it CAN work, you just need to take a different approach. I created a tutorial to show you how https://mastersketchup.com/solid-tools-components/