Baloo help file (link below) mentions that after deleting the index database you should set first run=false in the configuration file. That forces an automatic update again or on startup. It should be the other way around: set it true to indicate it is a first run. Could even be stated more readable in the conf file: this is first run: true [or false] https://community.kde.org/Baloo/Configuration
It is a matter of developer understanding for the help documentation produced.