If you have previously customized the Smart Instrumentation tool schema for a previous version, you will need to upgrade the latest INtoolsMap.xml file in order to preserve your custom changes.
Before removing the previous version of Smart Instrumentation, be sure to back up your existing INtoolsMap.xml file so that you do not lose your custom changes. The INtoolsMap.xml file is located in the path <Smart Instrumentation home folder>\XML\.