... if I 'save' the gallery, then all the images are deleted from the Small and Large folders.
Sorry. I should maybe have been more specific with my instructions.
(1) Create a Multi-Size Image gallery with JuiceboxBuilder-Pro (by selecting 'Resize Images' and allowing the application to create small and large images) so that smallImageURL and largeImageURL entries are included in the gallery's 'config.xml' file and 'small' and 'large' subfolders are included in the gallery's 'images' folder.
(2) Create three sets of images yourself in an imaging program (such as Photoshop) and replace the medium images in the gallery's 'images/' folder, the small images in the gallery's 'images/small/' subfolder and the large images in the 'images/large/' subfolder.
(3) Do not edit the gallery in JuiceboxBuilder-Pro after doing this. If you re-save the gallery with 'Resize Images' deselected, the smallImageURL and largeImageURL entries will be removed from the gallery's 'config.xml' file and the small and large images will be deleted from the 'images/small/' and 'images/large/' subfolders.
... are you certain that the gallery will actually *use/deliver* the small and large images when being used by the appropriate devices?
As long as there are smallImageUrl and largeImageUrl entries with valid paths pointing towards corresponding images (which, by default, will be in the 'images/small/' and 'images/large/' subfolders), then Juicebox-Pro will use the appropriate images (depending on the device, screen size, pixel density, etc.) when the gallery is displayed.
The key is to not re-save your gallery in JuiceboxBuilder-Pro with 'Resize Images' deselected after creating a Multi-Size Image gallery and swapping out your images.