Visaul Web Developer does not provide any automated support for converting a WAP to a Web Site. I'm afraid you have to do this manually. At the very least you'll need to convert the CodeBehind attributes to CodeFile and delete the .designer files. Depending on what else is in your project you'll have more work to do. If you have any web references, I'd suggest removing them before the conversion and readding them after. There are many other issues that you might encounter that are similar to the VS03 to VS05 Web Site model.
Even though this whitepaper is about VS03 to VS05 conversion it gives you an idea of the kinds of problems that could be encountered.
http://msdn.microsoft.com/asp.net/reference/migration/upgrade/default.aspx?pull=/library/en-us/dnaspp/html/conversionissuesasp_net.asp
The real complication is in converting from code behind, single assembly to the dynamic compilation model of ASP.NET. If you've recently converted from Web Site to WAP and now want to move back it should be fairly painless. If you've taken advantage of the fact that all code behind classes are in the same assembly and can directly access each other you've got more work to do.
Hope this helps,
Brad.