Please check to see if the missing files and folders are actually there but just hidden.
We had one other user report such a phenomenon about 5 months ago. Unfortunately, we were not able to determine the reason for the files and folders being hidden. JuiceboxBuilder-Pro does not set hidden attributes on any gallery files or folders. Maybe the cause is somehow due to the location the gallery is being saved to? Perhaps there are permissions on a parent folder which are somehow causing this problem? (This is just speculation, though. I really don't know why this might happen.)
If the missing files and folders are actually there but just hidden, then hopefully you'll be able to change their visibility via their properties.
I realize that this is an inconvenience but I hope it's at least a suitable workaround (even though it's not a direct solution).
If the files and folders are actually missing (and not just hidden), then this suggests that something may be preventing JuiceboxBuilder-Pro from writing to the gallery folder. If this is the case, then please check any anti-virus and security software that you might have installed to see if this is somehow interfering with JuiceboxBuilder-Pro's functionality. Also check that you are saving the gallery to a folder that has no restrictions, is not on a network drive and is not actively being synced to an online backup or file sharing service (e.g. Box, Dropbox, Google Drive, iCloud, OneDrive).