Great Question. I have the exact setup you have. I wanted two files of my MP3 for backup, etc.
Here is what I do weekly or more depending on the amount of changes that have been make to my "production database". I make all changes to one database then sync to the other.
I have moved my pointer databases from the jriver directory to my music directory.
First copy your database from the production machine to the backup machine (make sure both are in sync) Now copy your pointer files over as well. Remember the pointers will not show in the same drive letter (or maybe it will) Mine is production drive "D:\Music" with sub directories for videos, etc and my backup is "F:\music" Identical except for the drive letter.
Now that everything is copied over simply go to mediajukebox and
go to Edit, Properties, Tools, find & replace, "check" location box, enter in find-what "D:" (for production system) and enter into replace "F:" (for backup database location. Assuming your subdirectories are the same this will change your backup pointer to the correct area. All of your playlists, etc function correctly.
Now, go to
http://softbytelabs.com/Frames.html and download Comparator . This will allow you to sync from production to backup only the items that are new or have changed. The backup side that has new or changed should be deleted. If you have your pointer database in the tree structure it will automatically be synced also.
I use comparator weekly to sync my production to backup and then do the find and replace and all is well.....
This is great stuff.
If I can help please email me at garyvia@aol.com