not2easy - 6:20 pm on Sep 23, 2012 (gmt 0)
A noindex meta tag in a subdirectory's index.html file should not have any effect on other pages in the same directory, BUT that assumes that those pages do have some other pages somewhere in your navigation that links to them and that they are in your sitemap. Or you could make the pages more useful and let them be indexed as /directoryname/. If the pages you want indexed have inbound links and are in your sitemap -and don't have a meta noindex tag they should get crawled and indexed just fine without the index.html pages being indexed or affecting other pages.
I recently needed to do something similar for a site where the folders previously did not contain any html pages and an urgent site redo had me end up with pages I want indexed in those subdirectories where I had had a noindexed index.html for years. I'm slowly working the site into proper structure, but those index pages were being shown in the sitemap until I changed them to index.php files. Now they sit there doing nothing except covering lists of files from nosey things. When I'm done they will be indexed pages with the url of /subdirectoryname/