See the help topic: How To: Implement a Major Upgrade In Your Installer
Major Upgrades can only perform upgrades in the same installation context. (Per User -> Per User or Per Machine -> Per Machine ). If your VDPROJ was installed Per-User by accident then the user will have to uninstall / reinstall to become Per-Machine.
Your new installer doesn't have to have the same UpgradeCode as the old installer but it does have to author the MajorUpgrade using the UpgradeCode from the old installer.