To restore sites that are on live remote servers, to work from locally, I have imported site definitions and have begun to load the sites from the host servers. I want to restore from these from remote versions since I've noticed my local backups sometimes re-assign the link names (naming them to the locations of my drive being saved to, not 'http'. Also, when saving .xhtml sites MX has a tendency to change certain portions of the code, especially from the header on up).

I've noticed two folders within my local backups that don't seem to exist remotely:

_notes (containing mno files)

_mmServerScripts (containing MMHTTPDB and mysql php files for databases)

What should be done with these to help ensure a complete backup to work from locally?