Windows Installer Issue when Installing over Previous Version Application

Recently I worked on Windows Setup Project to deploy a new version of an existing application. The application and installer was developed using Visual Studio 2008. I'm using Visual Studio 2010 to work on the project. All of the projects including the Windows Setup are still using the same .NET framework and prerequisites.

When I try to install the application (it has a setup.exe, an msi and some other files that have been packaged together using IExpress) over the older version on a machine, a few issues occurred even tough the installer said that the installation was successful.

The issues were the application's shortcuts were disappeared and all unmodified files in the installation directory were gone, only the modified ones were still there. What I mean by unmodified files are the files that were exist in both version and have not been updated/changed in the new version.

According to these articles; http://connect.microsoft.com/VisualStudio/feedback/details/559575/problem-with-installing-and-removing-previous-versions-after-upgrading-my-setup-project-to-vs2010 and http://social.msdn.microsoft.com/Forums/en-US/winformssetup/thread/b87f1aea-d15a-484b-8cdc-0d212784f941/, the problem occurs because all of the files' component GUIDs are changed when the setup project is migrated from Visual Studio 2008 to Visual Studio 2010. A workaround for this is to re-sequence 'RemoveExistingProducts' right after 'InstallInitialize' in the installation processes sequence table of the application's msi file.

Here is the detail of the process:
1. Use 'Orca' to open the new version applicaton's msi file. 'Orca' is a tool for creating and editing Windows Installer packages and merge modules. 'Orca' can be downloaded from http://msdn.microsoft.com/en-us/library/windows/desktop/aa370557%28v=vs.85%29.aspx.
2. Right click the msi file then select 'Edit with Orca'.
3. Select 'InstallExecuteSequence' table on the left pane window.

4. Then on the right panel, find 'RemoveExistingProduct' in the 'Action' column, see the blue colour highlighted row.
5. Double click the 'Sequence' value (the yellow colour highlighted cell) then change the value to 1525.
6. Save the changes.

Then try the installation again.