Luzin's conjecture was widely believed to be false, until it was proven by Carleson in 1966.

I'm citing from Lennart Carleson's biography: "In 1913 Luzin conjectured that if a function $f$ is square integrable then the Fourier series of $f$ converges pointwise to $f$ Lebesgue almost everywhere. Kolmogorov proved results in 1928 which seemed to suggest that Luzin's conjecture must be false but Carleson amazed the world of mathematics when he proved Luzin's long-standing conjecture in 1966. He explained how he was led to prove the theorem:-

... the problem of course presents itself already when you are a student and I was thinking about the problem on and off, but the situation was more interesting than that. The great authority in those days was Zygmund and he was completely convinced that what one should produce was not a proof but a counter-example. When I was a young student in the United States, I met Zygmund and I had an idea how to produce some very complicated functions for a counter-example and Zygmund encouraged me very much to do so. I was thinking about it for about 15 years on and off, on how to make these counter-examples work and the interesting thing that happened was that I realised why there should be a counter-example and how you should produce it. I thought I really understood what was the background and then to my amazement I could prove that this "correct" counter-example couldn't exist and I suddenly realised that what you should try to do was the opposite, you should try to prove what was not fashionable, namely to prove convergence. The most important aspect in solving a mathematical problem is the conviction of what is the true result. Then it took 2 or 3 years using the techniques that had been developed during the past 20 years or so"