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If you use the "Add Book" option in Calibre and the book already exists in Calibre, then the Add will probably do nothing as it would be deteced as a duplicate. That would explain your DRM warning as you were still getting the previous version.
If you want to replace an existing format of a book, then as was mentioned the way to do it is to use the Edit Metadata dialog, and there add the replacement to the Formats section of that dialog. You can add it either via the button, or via drag-and-drop. That way of operating will overwrite any existing format of the book if it already exists, and add it if it does not.
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