If you are unable to open your gallery in JuiceboxBuilder-Pro, then, as long as your images and thumbnails have the same file names, try the following:
Copy your gallery folder.
In the copied gallery folder, replace the images in the 'images' folder with the images from the 'thumbs' folder.
Now open the copied gallery folder in JuiceboxBuilder-Pro (which no longer contains all your large images).
Re-order the images in JuiceboxBuilder-Pro ('Images -> Sort -> Reverse') from the drop-down menu at the top.
Save the gallery on the 'Publish' tab.
Replace the 'config.xml' file in your original gallery folder with the 'config.xml' file from the copied gallery folder.
If this does not work (for example if you are still unable to open the gallery in JuiceboxBuilder-Pro), then if you know any programming languages, you could perhaps write a script to reverse the order of <image> tags using XML parsing techniques.