It was difficult to eliminate karma, not to mention in the Qianyuan world that had been conquered by an alien immortal. Even if the immortal patriarch had transcended, the sect and the disciples were still there, so the karma naturally still existed.
Fu Yunzi understood this point from the very beginning. Otherwise, he wouldn't have taken out the highest heaven magic sword. This magic sword would trigger karma during the Tribulation.
This was also the source of Fu Yunzi's unending disaster aura. If he didn't bring the allheaven magic sword, Fu Yunzi wouldn't be able to trigger his teacher's karma. If he used an item that could cover the sky or obscure the secrets of heaven, he might be able to split the disaster.
But he didn't do so, because Fu Yunzi left all hope to Chen jingzhai. He was actively helping Chen jingzhai to cut off the karma and clear the path ahead. His goal was for Chen jingzhai to seize the opportunity to enter the secret realm two hundred years later.