Why doesn't Visual Studio refresh the folders when I click the Solution Explorer refresh button?
At the top of the solution explorer is a toggle button "Show All Files" this makes it include all files in the display even if they aren't included in the project. The icons for these will be grayed out a bit. Then just use the context menu to add these to the project.
On the solution, click the right mouse button and select 'Add existing item' and pick the file from the solution root directory. The Solution will now get a 'Solution Items' directory which contains your file. This directory is virtual, so it does not exist on disk.
However there is no feature like 'Show All Files' for a solution, this only works on projects.