How to upgrade the manually installed backup agent
Copy the backupagent.msi file from the installation download package to the domain controller. Run the .msi file while the existing backup agent is installed. This will take care of the uninstall of the old version and the install of the new. This does not require a reboot of the domain controller.
Review the Upgrade and Compatibility section of the release notes to ensure the existing version is part of the supported upgrade path. If it is not, uninstall the existing agent from the Add/Remove Programs and then install the new version.