When installing a major upgrade of an InstallScript MSI project, all system changes done via InstallScript (i.e., registry operations, file operations, shortcuts) are rolled back at the end of the major upgrade. This means that it may even delete items that are in the newer version.
For example, if version 1 had registry entry A, and version 2 had registry entries A and B, after upgrading from 1 to 2, only entry B is on the system. Even though version 2 installed entry A, the rollback of version 1 wipes it out.