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Assuming the option is still there, check the box Settings / File names / Use book ID as filename. One purpose of the option to solve the problem(s) you present. In this case 'ID' means the book UUID (long unique identifier) for the book. The UUID is preserved even if you must rebuild the library or move (not copy) the book to another library.
Another and probably better option is to use subfolders. The CC FAQs have gone away, but here is the content of an old FAQ that discusses using subfolders to solve exactly the problem you raise -- how to get more books in a FAT32 library.
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