You can replace a photo in Lightbox, using the Tools button. The Lightbox can be accessed both via the gallery and the Photo Organizer:
via Photo Organizer
via Gallery
Lightbox
IMPORTANT: if a photo is used for an order, there is a link between the photo and the order. So if the image is simply deleted and a new version is uploaded, that link breaks and the newly uploaded version will not be linked to the order, automatically.