You must make sure at all costs that the uninstallation uses the same JDK / JRE which you used for the installation.
If that won't work, then the only ways are:
- uninstall using some Windows tool and something like CC-Cleaner (registry cleanup tool),
- reinstall Windows from scratch on that machine and then only install the correct version.
Never ever try to run one installation on Windows in location A when there is a second installation in location B if the uninstall process for location B failed (as in your case). That's a very good way to mess up your Windows system completely.
Sorry that I don't have any better news. That's my experience. Maybe Windows 2016 is better than 2008 when it comes to remove unwanted software, I don't have much experience with 2016; but with older Windows versions I often encountered really nasty issues if I did not remove one software component completely (including a reboot) before trying to re-install.
Thanks Nico. I kind of had the same thought, and opted to start over with a server snapshot taken before any installations. I will be reinstalling and reconfiguring PowerCenter as well as PowerExchange, and I will get more snapshots along the way this time. But I agree it was not worth risking messing anything up long term or short term.