Typically, an application level display refresh involves redrawing a screen based on the most recently available raw data, as opposed to a display buffer. Thus if you refresh your desktop on Windows or in explorer, it might take slightly longer than a similar redraw, but is more likely to have a more correct, i.e. up to date, result.
For example, if you are showing a shortcut to a network item that has been changed remotely, that update may not be reflected on your screen without a refresh, even though your screen has been redrawn, e.g. by minimizing an occuluding window.
More commonly, we see this in internet browsers, where the display is typically recreated from a local cache, whereas a refresh will rebuild that cache and redisplay based on the most up to date remote data. Again, this may be slower than a simple redisplay.