The MSI installer uses a unique GUID generated when the distribution kit was originally created. It doesn't look at the application or project name to determine who to uninstall.
It sounds like you copied one project file and renamed it before making your other changes. Renaming files doesn't change the GUID.
To solve your existing problem, close CVI, then use a text editor to open the .prj project file for one of the projects. Look for the line that starts
Distribution Kit GUID = . Delete this line, resave the project file, and exit the text editor. Start CVI, open the project whose file you just edited, and rebuild the distribution kit.
In the future, rather than copying a project and renaming it outside of CVI, select File >> Save Project As... from the menu.
If you save your project under a new name (using File >> Save Project As... in the project window) , you'll get a new GUID when you build a distribution kit using the new project.