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Best thing is to stay out of library folders and its sub-folders.
The calibre software can do everything you need to do and maintain integrity between the library folder tree and the database. Using a file manager to add, rename or delete folders/files in a library won't do that.
I have several libraries with up to 150K books, I run library check on them weekly. I get very few errors, when I do get one I can invariably put it down to something I did within the last week. And because I know what I did I know how to fix it.
BR
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