Trying to change the filename of the MSI and performing a minor upgrade is not supported. See:
Windows Installer Best Practices
Keep package names and package codes consistent.
The .msi file can be given any name that helps users identify the package, but the name should not be changed without also changing the product code.
•Give your .msi file a user-friendly name that enables the user to identify the contents of the Windows Installer package.
•The product code is the principal identification of an application and must change whenever there is a comprehensive update to the application. For information, see ProductCode and Changing the Product Code. Changing the name of the application's .msi file is considered a comprehensive change and always requires a corresponding change of the product code to maintain consistency.
•The package code is the primary identifier used by the installer to search for and validate the correct package for a given installation. No two nonidentical .msi files should ever have the same package code. If a package is changed without changing the package code, the installer may not use the newer package if both are still accessible to the installer. The package code is stored in the Revision Number Summary Property of the Summary Information Stream.
•Note that letters in product code and package code GUIDs must all be uppercase.
The product code must be changed if any of the following are true for the update:
•Coexisting installations of both original and updated products on the same system must be possible.
•The name of the .msi file has been changed.
•The component code of an existing component has changed.
•A component is removed from an existing feature.
•An existing feature has been made into a child of an existing feature.
•An existing child feature has been removed from its parent feature.
Why does changing the name of your MSI file require a Major Upgrade?