Yes, a partial solution. It seems you can select multiple folders of the SAME color tag, right click on one of them and click on the appropriate color to remove and all selected folders of that color will have the tag removed.
Now here is the weird thing. For example, one red tag folder and two yellow tag folders. Select all, right-click and click on the yellow tag—a yellow tag is added to the red tag folder (didn't know you could double-tag :o). Now, here is the amazing thing, select all folders and right-click and click on the yellow tag and all yellow tags are removed. This leaves you with 2 clean folders and one red tag folder. You could repeat this process of adding and removing specific color tags until all folders have no tags. Of course it might be easier to sort the folders by tag color and just remove the same color tag from the same folders. With hundreds of folders, as you say, what works best might depend on how many different colors you have in your tags.