Amon controls Malignus while Nova is at 20 life. He casts Essence Harvest, targeting Nova.

Nova loses 10 life, which reduces Malignus' power to 5. Does Amon gain 10 life, or only 5?

Amon will gain 10 life.

Essence Harvest determines the value of X it's going to use as it starts to resolve, and that value won't change in mid-resolution after that, even if the greatest power among creatures Amon controls changes during the process of resolving the spell.