It's hard to say, maybe they just built better for knock out stage and found confidence just in time.
But also the few games I saw, mainly two things changed:
1. He completely stopped using Ramos, the traditional CF, in the rotation. Nonstop just the wingers. Same thing with Zaire Emery stopped getting starts (less of a passer and more of a hardworker), and became the two Portuguese wizards and Ruiz full on for midfield trio.
2. He stopped tinkering with the formation, sometimes he used 3412, 4212, 352 etc in big games/when rotating. Even if it was mainly 433, after January it became solely 433. They truly mastered that set up. It also helps they stopped getting injuries to their defense line.