They thought decreasing numbers were due to birds dying, but they were actually due to birds changing breeding locations (for unknown reasons).
Basically, and contrary to the headline, the article says they don't know enough about penguin breeding behavior to draw any conclusions.
"Over five years in the late 1970s, the Southern Ocean warmed and at the same time the penguin colony at Pointe Géologie, declined by half (6,000 breeding pairs to 3,000 breeding pairs). The decline was thought to be due to decreased survival rates. In other words, researchers thought that the warming temperatures were negatively impacting the survival of the species...'It’s possible that birds have moved away from Pointe Géologie to these other spots and that means that maybe those banded birds didn’t die,' LaRue said. 'If we want to accurately conserve the species, we really need to know the basics. We’ve just learned something unexpected, and we should rethink how we interpret colony fluctuations.'”
P.S. Want to know why people are skeptical about climate change "science" and advocacy? It's because of blurbs like this one that say one thing in the headline and something else in the linked-to article.