The adult sea emperor was too old to produce enzyme 42 in potent enough amounts to give a cure. The emperor gave the info on how to make hatching enzymes to encourage her eggs to hatch. Her offspring produced enzyme 42 naturally.
As for how a cure was made in BZ, well the obvious answer is plot hole, but we could say that after scientists were able to study enzyme 42 itself they were able to work out the exact properties that cured the infection & so worked out how to extract such properties from other flora & fauna on the planet.