I think one question that comes to mind is: if there is already a file in the folder, how did it get in there? If it was placed there by your user, he should already be aware that there is a way to drag and drop files, as he will have seen the dashed lined area that you described.
If that isn't the case, you could go with a small text note either inside the droppable area or above it. You could even place the whole dashed line under the existing elements, given that there is still space left. Undoubtedly you'd have to make some sort of visual signification.
Another thing you could do is placing an upload button (which you should have either way to give your users a possibility to upload files the usual/classic way) somewhere in your GUI which will trigger a modal dialog containing the dashed lines with a note that you could either drag and drop files there or hit a "Browse…" button that will trigger the default process by the browser. That way you can establish your drag and drop functionality in a more context oriented way, without having to fill up space in your GUI.