You could use a "staging" library, and use the right-click "Copy to library" action to move properly-organized books to the main library once their metadata meets your approval.
Import chunks, tag them properly (maybe, assume all current books in library are from xxx genre? easy to fix that in bulk), then use Copy To Library (Delete After Copy) to clean up and get ready to import a new batch.
Or, as long as the ebook has the metadata properly embedded in the ebook file itself, calibre will recognize those metadata Subject tags (for genre) and author/title/etc. metadata as applicable.
But I am going to guess based on your failure that the metadata (certainly genres) isn't embedded.
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Alternatively, see the Preferences ==> Adding books settings. You can choose to derive metadata from the filename rather than file contents.
Set a suitable regular expression based on your current file/folder organization.