You are basically not doing things properly and you want to do a wrong thing. In .NET you can use ClickOnce, that can do this for you, using MSI package you can create a new update MSI package to upgrade existing installation see here how. That would be a standard and correct approaach.
However if you just need to hack the version displayed in control panel, you can edit your app entry under following registry hive:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Uninstall
or
HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows\CurrentVersion\Uninstall\
There you just edit the DisplayVersion
string value to whatever you want for whatever reason. But if your installed MSI is just a bootstrapper, I do not see any reason to hack its displayed version number.