Atari and movement
The action of popping a finger or a thumb off and onto an open or closed hole is called atari. It is used in shakuhachi playing to repeat a note when the score calls for a repeat and is idiomatic to shakuhachi playing in that it introduces a split second of a higher or lower pitch into the air-stream. The physics of the flute are such that only the slightest movement of the finger off the hole is needed to create the desired effect. This often means the finger barely breaks its fleshy seal with the hole. If the movement is too overt, then the flute may be jolted and your embouchure discombobulated. If the movement is too slow, the modulation becomes a note triad.
When holes are not being covered, those fingers should be well away from the holes and in fact, they should be raised as high as possible in relation to the fingers actually covering the holes. This is the sectret to being able to play fast passages on a shakuhachi.