For anyone interested.
I have made the changes to the
external tool this question was related to.
Not using albumfiles.txt to create the objects in the project, but using the code posted above, means the mirrored project does not reflect the ordering of objects in the original project.
Steps now used are:
Loop through the original project make a list of all of the objects files paths as strings.
Create the folder structure for the mirror project to use.
Copy any page template .info files to the mirror
Import (copy) the project settings file.
Load the mirror project (just empty folders for now)
Loop through the list of file paths and create album objects from each file path
Ask if the original project should have jAlbum specific files removed, and if so do it.
Thanks to everyone who has helped me learn a bit more Java.