Everything except the window sizes & positions is stored in your TCMD.INI. The window layout is stored in the registry (HKCU\Software\JP Software\Take Command 18.0).I was installing into a new setup, and copied my "old" TCMD folder from a backup onto the new Windows 10 install. Then I tried re-installing into the same folder and got the error.
That wouldn't be a major issue if I knew what folder or items hold all the setting info (fonts, colors, prefs, etc.) to back up in order to have in case I needed to to restore at a later point.