Sometime, when adding a directory with audio files in a directory included in the list of directories indexed by Baloo, they are not indexed. Executing balooctl check fix that. Using balooctl status show the files inside the directory in the "scheduled" state.
I have identified one way to reliably have files not being indexed by baloo. Follow those steps to reproduce: * have a laptop with a power cable plugged in ; * unplug the power cable: the laptop is running out of battery ; * create some new files that would normally be indexed by Baloo: nothing happen, the file indexer is suspended when in battery mode ; * plug the power cable: nothing happen. In this cable one expects that baloo would pick up the waiting to be indexed files as soon as a power cable is back. As far as I have seen, it is not the case. A possible workaround is to use balooctl suspend ; balooctl resume sequence of commands.
Looks like this was fixed by https://cgit.kde.org/baloo.git/commit/?id=f8897a2511c4652c203bf25f6d788d0a698e4203! When indexing starts up again, it now checks for unindexed files.