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I'm not sure I understand what you're trying to do; would it be possible to post a packaged workbook so we can have a look?
One possible solution you might want to try is use a dual axis, with the marks on top, and only show these whenever "Country" is selected. Make sure their opacity is at 100% (not transparant), so they'll cover up the colors. For marks where you don't want to show a flag, you could create a blank .png object (remove the background, so it'll become transparant).
Hope this helps!