Any reason this code would changing the resolution of the original JPEG? I can understand if the file size were different because the JPEG quality settings are probably different but I don't understand why this would be resizing an image.
File newfile=new File(mydestinationfolder.concat(imagename));
Files.move(file.toPath(),newfile.toPath(), REPLACE_EXISTING);
Rotation Orientation;
if ((Orientation=Exif_data.get_Exif_Orientation(newfile)) != null) {
System.out.println(Orientation.toString());
BufferedImage oldimage = ImageIO.read(newfile);
BufferedImage tmp = Scalr.rotate(oldimage, Orientation);
oldimage.flush();
oldimage=tmp;
ImageIO.write(oldimage, "JPEG", newfile);
}