Not necessarily.
From the article you posted
Historian John M. Barry, who wrote The Great Influenza, a widely read chronicle of the 1918 pandemic, rejects the view that the two pandemic waves in 1918 were caused by different viruses. Barry was also the first author of a 2008 study of flu patterns in US Army camps in 1918, which suggested that those who were infected in the first wave had protection from both infection and death when the second wave came.
“I think all the evidence, both epidemiologic and now molecular, points to the opposite conclusion of this [Lancet] paper,” Barry told CIRAP News. “I think the evidence strongly suggests the same virus caused the spring and fall 1918 waves. They say the spring wave protected against death but not against infection. That is not correct. We found up to 94% protection against illness—a somewhat higher level of protection against illness than against death.”
Even if it were true that infection in the first wave conferred protection against death but not illness in the second wave, Barry said, “Protection against death is hardly evidence to support an argument that different viruses caused the different waves. That is a very tortured argument. And of course the recent PNAS [Taubenberger] paper found molecular evidence that the same virus caused both waves.”
Barry also took the researchers to task for saying they are unaware of other cases in which circulating fu viruses showed sudden changes in pathogenicity. In the pandemic of 1889-92, he says, the third wave was the most lethal, adding, “Possibly those three waves were caused by different viruses, but we don’t know that. You can’t simply define it away and reject it as a precedent because it doesn’t fit your premise.”
Another case in which a circulating flu virus might have abruptly become more pathogenic was the flu season of 1951, when a seasonal H1N1 virus caused the deadliest influenza year of the 20th century, other than 1918 to 1920, Barry said.