Really good use of such a simple mechanic, each boss has it's own unique way that interacts with it, making the fights pretty interesting and memorable. It's more of a nitpick than anything, but I think a sound effect or visual indicator on the boss for when the damaging phase is about to end would be nice, I'm usually too focused on hitting the boss to notice how much time is left on the hourglass and occasionally take damage cause of it (skill issue).
It's a very well made game that I had a lot of fun playing. And the subtle music changes were a nice touch. Great job!