Per the entry at AppDeploy.com, Endnote 10.x uses the Windows Installer natively for its installation. This is a Good ThingTM.
It's unclear to me if Endnote 9 uses Windows Installer or not. 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.
If the Endnote 9 doesn't use Windows Installer you're at the mercy of their uninstallation program re: performing a silent uninstall. 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. It'd be some work, but with potentially up to 500 machines the time savings would probably be worth it.
Ultimately, without seeing the application firsthand I can't give you any kind of step-by-step process. This is a good high-level overview of the process you'd need to apply. In a world where all these machines are joined to an Active Directory domain I could see this getting done in 6 - 12 man hours (less if Endnote 9 is MSI-based, more if the Endnote 9 uninstaller behaves poorly for your needs). That'd be a heck of a lot easier than visiting 500 PCs...