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Does that "main page" you mention link to the files by their current name? If so, try downloading that, verify that the links are intact and lead to the local copies of the articles, then stick that main page into Calibre. It should then gather up all the articles and you can convert a single book containing all articles at once.
There's no way you can batch rename those files with the tools Calibre provides.
Edit to add: You can, of course, simply use your "sub-library" idea by using a saved search that finds those articles to restrict the library view.