Use the Manual Mode upgrader and skip this step by changing the step number in the URL. If it was an unused Lite install then you don't really need it.
If you are right and the Lite version was not fully uninstalled before, hopefully the installation is okay after the upgrade. It can be hard to tell if the partly-uninstalled state will have a negative effect in the end. Right now it is just making the upgrade difficult with some errors because the previous version number is not known.