Microsoft has release an update for Microsoft Visual Studio 2010 Service Pack 1

When you install the .msi file that is created from the Visual Studio 2010 SP1 Setup project, the .msi file determines that the GUID has changed. Therefore, the .msi file removes the files and registry keys for the installation path by using the sequence of the project. This issue occurs because a different hashing algorithm is used to create the Globally Unique Identifiers (GUIDs) in Visual Studio 2010 SP1.

To resolve this issue, apply this hotfix, and then set the new BackwardCompatibleIDGeneration property to True before you build the project.

This hotfix introduces the BackwardCompatibleIDGeneration property. By default, this property is set to False. Before you build the Setup project in Visual Studio 2010 SP1, you have to explicitly set the BackwardCompatibleIDGeneration property to True.

  Update for Microsoft Visual Studio 2010 Service Pack 1 (KB2529927)