A: Google will treat the links that are no longer in the file as dofollow again, removing the nofollow over rule the file provided.
My Thoughts: So basically if you made a mistake and put a link in your disavow file, it is not treated as a nofollow forever it will only remain nofollow as long as it remains in the disavow file or is changed on the actual website itself.
I think the question being ask was misunderstood by John, the question really was, once I have got out of a manual penalty should I remove all my links from the disavow file. The real question that comes off the back of that is, what would happen if you did that? Would it trigger an unnatural links warning again?
A: Yes and NO, Mostly yes, if Google is aware of a page that is very popular and of high quality it can still rank well, but it could rank better if the penalty is released. If new content is created it will likely be surpressed by the penalty
My Thoughts: Get the penalty sorted out, do not try and SEO your key pages out of the Penalty, its an uphill battle to do that.
A: John says Yes
My Thoughts: The real question that we all want to know is not answered, if the page has bad quality content but has page rank and ranks for some longtail keywords, noindex is a bad idea, should it just be left as it is and fixed as soon as possible. Or should that content be removed from that page until it can be re-written?
A: Yes. You can also use the date feature on an XML sitemap as well.
My Thoughts: Another way not mentioned by John is to use a Webmaster Tools feature called "Fetch as Google" in the health section. Put the address of the page in the form and hit "Fetch" it will appear below and you can then clikc submit to index and Google will index or re-index that page as a priority.
A: John says NO
My Thoughts: I think if you have dofollow links active on comments then you will run into problems.
A: Yes, removing low quality content will be noticed and will fix the site.
My Thoughts: John mentions about this article "More guidance on building high-quality sites", it is worth looking at.
A: John says contact him on Google+
My Thoughts: John really does look at the requests sent to him.
A: The disavow file is looked at by a real person for manual action reviews and also used by the Google algorithm
A: No, it is unrelated
My Thoughts: All those files will be crawled to see if they noindex or Canonical has changed and if so would be re-indexed.
A: NO, but it is not optimal.
My Thoughts: It is not clear if your site will suffer from Panda as a result of large duplication it.
A: Yes, can be indexed and can show up in search results.
My Thoughts: John also mentions it is worth looking at 5 common mistakes with rel=canonical