If you have a copy of the gallery folder on your computer's hard drive and your gallery uses a regular structure (i.e. does not use a configUrl or baseUrl), then you can open and edit the gallery in JuiceboxBuilder-Pro.
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).