I think $HOME/.config/baloofilerc is used by baloo-kf5, while $HOME/.kde/share/config/baloofilerc was used by older baloo (so if you switched to baloo-kf5 you can remove the second one). In general, I noticed that quite a number of KDE related config files moved to $HOME/.config from $HOME/.kde/share/config.
Regards, Hillel Lubman.
