After official launch of Visual Studio 2010 in Las Vegas, Microsoft has highlighted incompatibilities of Visual Studio 2010 Express for Windows Phone CTP (Windows Phone Developer Tools) with Visual Studio 2010 RTM.
If you install the retail (RTM) release of Visual Studio 2010 on the same machine on which you already have the Windows Phone Developer Tools CTP, you will be unable to build your Windows Phone projects. Further, while the Windows Phone project type will continue to appear in the File/New dialog, you will not be able to build Windows Phone 7 applications.
The current CTP is based on Visual Studio 2010 RC; reason being that updates made to Visual Studio RTM since RC release, are causing some incompatibilities. Visual Studio 2010 Express for Windows Phone (WPDT) has different Development Life Cycle than regular Visual Studio release and exclusively targeted to Windows Phone 7. Microsoft has also assured the an update will be made available in coming weeks to resolve the incompatibilities.
Meanwhile, if you want to avoid this issue and want to use Visual Studio 2010 RTM then you can either install Visual Studio 2010 to a VPC image or on another machine, because installing WPDT CTP to a VPC image is not supported.