The 'Add Juicebox Gallery' button will add a Juicebox gallery shortcode to the page or post but there is no code in the plugin which can change or remove an existing shortcode.
Also, there is no code within the plugin that can delete any images from a gallery (or the WordPress Media Library).
All image handling is performed by core WordPress code. WP-Juicebox just displays the images that happen to be attached to the page or post containing the gallery at the time the gallery is displayed.
The plugin also does not contain any scheduled tasks (which might make things appear to happen on their own).
It sounds like something other than the plugin might be at the root of your problem.
Ask everyone who has administrative access to your WordPress site if they have done anything which might have changed anything.
Also, check in with your web host to see if they have experienced any problems recently and have had to backup your site using older versions of your files.
Hopefully some investigative work will help to point you in the right direction.