The wrong phrase was used in this case. When it says "Processing Project Tools notes" it really means "Processing posts" and vice verse. Considering that, is it a more accurate number.
Because we created a link DM for 2.1.0, this process is a bit more efficient. As a result, we have increased the default number to process per page from 50 to 200. On some of our tests, it is still possible to run over 1000 queries on a single page load, although for most pages this number is between 10 and 20. At this rate, you should be able to finish your 400,000 posts in 1 to 2 hours. You should not ever have to run the tool again if all goes well.
The misused phrases have been fixed.