This is a good high-level overview of the process you'd need to apply. Ultimately, without seeing the application firsthand I can't give you any kind of step-by-step process.

It'd be some work, but with potentially up to 500 machines the time savings would probably be worth it.

If their uninstaller absolutely won't uninstall silently, with this number of machines, I'd consider snapshotting the machine's 'before' and 'after' states when uninstalling and writing a script that performs all the functions of their uninstaller silently. If the Endnote 9 doesn't use Windows Installer you're at the mercy of their uninstallation program re: performing a silent uninstall. If it does, then you've got an easy solution using either Group Policy (if these machines are joined to an Active Directory domain) or a script to use MSIEXEC to uninstall the old version and install the new version.

It's unclear to me if Endnote 9 uses Windows Installer or not.

Per the entry at, Endnote 10.x uses the Windows Installer natively for its installation.

Install endnote x2