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Sailor Sue - the safest way to maintain a separate folder structure is to use the Save to Disk feature, in which you would use a
Template to define the required folder structure.
As you appear to have discovered the hard way: within a calibre library you shouldn't change the structure of the folders and files, or change their names. My advice regarding calibre libraries is 'look but don't touch'.
However, try asking yourself this: "What will I do with a mega/master folder that I can't do via the calibre GUI?"
BR