I used FrontPage 2000 extensively in the past but have not used it much for the last year or so and have forgotten some of it's features. If you right click on a normal folder in FrontPage, you'll probably see an option to "Convert to web" and, conversely, if you right click on a web folder, you'll probably have an option to convert to (regular) folder.
Again, I don't recall the significance of this. But, surely, it is significant or the feature would not exist. My guess is that's it may not be significant when you're simply working on html files in FrontPage, but it may be significant when you publish your pages to host server, and perhaps even when viewing the pages on your own computer via your browser.
An good place to get some expert advice on FrontPage is a newsgroup, such as microsoft.public.frontpage.client. You can use Outlook Express as a newsgroup reader. And, check out the
FrontPage Users Forums.