On the 'Images' tab, you can rearrange images by file date or filename (if you need to) via the 'Images -> Sort' options from the drop-down menu at the top of the application.
You can then delete images (individually, of in a Shift-Click block or a Ctrl+Click selection) via Ctrl+D (or 'Images -> Delete' from the drop-down menu).

If you save the gallery to the original folder, the deleted images will be removed from the 'images' and 'thumbs' folders so, first of all, I'd make a backup copy of your master gallery and, each time you make a smaller gallery from the master gallery, open a copy of the gallery folder in JuiceboxBuilder-Pro (or make sure that you save each smaller gallery to its own new empty folder).

In doing this, you should be able to make several smaller galleries from your large one.

Otherwise, you'd need to edit your gallery's 'config.xml' file in a plain text editor and manually remove <image> entries corresponding to the images you'd like to remove (and also remove the corresponding images from the 'images' and 'thumbs' folder).

I hope this helps (although, even using JuiceboxBuilder-Pro, I realise that it could be quite a time-consuming task).

I have searched and not found an answer.

I have over 3,000 images in one gallery, is there any way that I can split this gallery into two or more galleries.

It was foolish of me to get into this position, a solution short of deleting and starting again would be very welcome.

Thanks.