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AFAIK, Google does count the links towards page rankings. Moreover, Google may start to include the anchor in a rich snippet in the search results. I would defer to what is best for the User in terms of linking, and it seems like using #anchor is going to be the right thing in the long run.

Thanks. I fetched both the main page and made a slight tweak to the robots and resubmitted last night. It looks like it is making a bit of progress. There is nothing else blocking the pages. We did add a new sitemap when we first launched the pages with no warnings. I did notice yesterday that we had approx 268 broken links that went to 404 pages in WMT in this specific sub-folder. The discovery of the broken link-404 pages by Google seems to be around the same time Google stopped crawling this section of the site. We took care of the broken links this morning. Thanks for the help!