Stopping the application won't work, the users will just a not found error. You should set the default document for the site appropriately, i.e, remove all others except your default html
http://learn.iis.net/page.aspx/203/default-documents/[
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A "better" way, however, would be to have a testing/staging site to update then migrate to production. The production site would be offline for minutes not an entire day.
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