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One thing the istaller installer does not handle properly is a straight uninstall, which appears to hang. As a result, upgrades can't be done directly. Instead, you should remove the existing version by using the "Change" option in the Add/Remove Software list, and then select Remove from there. You should usually reboot at this point.

Once this is done, you can do a reinstall of the new version to the same directory without damaging any existing configuration files.

It is recommended that you install the software to C:\opt\shibboleth-sp if possible. The installer may not default to this drive letter.