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In a word no, the folder structure and the folder and file names within calibre are determined algorithmically from the metadata.
You could add books to the calibre library in batches and remove from current location as you go, and I mean remove not delete to rubbish/trash/recycle bin.
But IMO it would be better if you got an external drive, I would imagine a 1TB usb drive could be had for less than ₹5,000 where you live. Move your 500 GB of books onto it, and then once you're satisfied they are safely stored in the calibre library you can use it as a place to backup your calibre library.
And even then you should not try to add all the books at once, do it in batches especially if you want to resolve duplicates as you're building the library.
BR
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