I am afraid that if I use the URL removal tool I might get the whole site out of the index. See:
Does this only apply to www. and non www. versions of a site or might this also affect subdomains? I don't dare to make the test!
I can't 301 redirect nor make those pages return a 404.
I could also insert in those pages the noindex, nofollow tag but I'm not sure if this would solve the problem of the already existing duplicates in the Google index.