Okay I tried it but for now the hot fix which worked for me is forcefully reinstall every thing when done with uninstalling.
<Property Id="REINSTALLMODE" Value="amus" />
The overriding throws a warning while building the WIX project. Property ID is a child of "Product" tag.
And as the Mirosoft WIX documentation said
Be aware how the Windows Installer applies the File Versioning Rules when Replacing Existing Files. The Windows Installer first determines whether the component's key file is already installed before attempting to install any of the files of the component. If the installer finds a file with the same name as the component's key file installed in the target location, it compares the version, date, and language of the two key files and uses file versioning rules to determine whether to install the component provided by the package. If the installer determines it needs to replace the component base upon the key file, then it uses the file versioning rules on each installed file to determine whether to replace the file.
Hence left with no choice, but to forcefully over write that.