Why are master zacharius's clocks not working anymore?

Answer 1

Each clock is a metaphor. Master Zacharius believes that the human body is as simple as a clock whereas the spring is the soul and the regulator is the body. He puts so much of himself into each one of these watches and clocks that when his body starts to deteriorate, so do the clocks. One line even states that he matched the regulated tick of the clocks to his own heartbeat. Although he believes that he is dying BECAUSE the clocks are dying, in reality it is the other way around. It is similar to a Hulcrux from Harry Potter, but in reverse.

Answer 2

Master Zacharius's clocks are not working because his daughter, Anaïs, removed their heart springs in an act of revenge after he forbade her from marrying the man she loved. Anaïs believed that by doing so, she could make her father repent for the pain he had caused her.