Well, first of all, the image will be demagnetized, the black and white levels adjusted, the white balance adjusted and a tone curve applied. With 16 bits to play with, most of this can be adjusted later without much problem – but that is with loss. Demosaicing is irreversible. These are not metadata, but it is important to know.
Second, there is information stored in something called "manufacturer notes". This often involves items such as the selected focus point, face detection information, and other non-standard metadata. Sometimes this is even encrypted. Some programs will ignore it completely and will not copy it to your new file.