Note entry switches to hidden voice from Piano part.

Perhaps it is better: First enter the notes then you can hide empty staves
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But there is something that I do not catch :(

Indeed, it is usually best to wait until the very end to hide empty staves, otherwise it can be disorienting as staves become empty or non-empty as you edit and staves suddenly disappear or appear as you edit.

If I understand you correctly, you are adding a note at the end of bar 59 - eg, select the eighth rest at the end of the measure, in the top staff of the piano part enter note input mode, press E. At that point this measure no longer fits on the same system as bars 55-58, so it moves to a new system. Since this is the only staff with notes, it is the only measure that displays. You might be thinking this is the flute staff, but it is not - it is the top staff of the piano part. The playback and the status bar both confirm this.

I think you are getting confused by the fact that ypu actually have a whole lots of completely empty measures that are disappearing completely because of "hdie empty staves". Notice, before adding this note, the score jumps from measure 59 to measure 92. That's because bars 60-91 are present but completely empty in all staves and so they are hidden completely. When you add the note to the end of bar 59, it moves to a system along with bars 60-72, but the other two staves (the flute and the piano bass clef) staves are both empty. Measure 73-89 are still completely empty and thus completely hidden.