Let’s test with Kodi default settings. Enter the following commands with an SSH connection.
systemctl stop mediacenter
mv ~/.kodi ~/kodi.bak
systemctl start mediacenter
If needed you can restore:
systemctl stop mediacenter
mv ~/.kodi ~/kodi.bk2
mv ~/kodi.bak ~/.kodi
systemctl start mediacenter
If your original setup was restored as expected and you want get rid of the unneeded clean install you can delete that with the following command.
rm -r ~/kodi.bk2