The file is not supposed to be in c:\windows. That file manages the tree and folder structure displayed in SAP Logon, and it's normally found alongside saplogon.ini, in the same folder. The default folder for it is going to be under %appdata%\Roaming\SAP\Common, but in an upgrade scenario the program tries to maintain the settings and locations from the older SAPGUI installation. In older GUIs the configuration files were kept in c:\windows, and then later they were kept in %programfiles%\sap\frontend\sapgui, but both of these were poor choices from Vista onwards due to the operating system protecting those locations. So, Jude is right, it's probably better to uninstall and then do a fresh install and avoid these issues.
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