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Sorry I'm confused as to what the problem is?
If you point Calibre at G:\Ebooks, then yeah it will try to import everything. If G:\Ebooks contains 20 folders each of which contains many subfolders, then you could point it to each of those 20 folders as a "batch". You can add new top folders or work at a lower level if that is too many for your "batch".
If you mean that some subfolders need to be imported as "one book per folder" (like an html version of the book with multiple pages), and others contain "many books per folder" then I believe you do have a problem. What I do is move the "one book per folder" books out into their own subtree that I can import using the different Calibre menu option. I automate this with a tool that walks the folders looking for this scenario.
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