Lava Jato was a general and surprisingly non-partisan anti-corruption investigation that took down a whole chunk of the Brazilian political scene from left, centre and right, because corruption is endemic in Brazil. And it removed some remarkably toxic scum.
Yes, it does appear that Lula was dubiously taken down as well, by a judge who wanted to win brownie points. However, in its defence, prosecutors have gone for Bolsonaro's associates too, including his sons. Bolsonaro has therefore declared that Brazil is corruption-free and is winding it down; there's little appetite in the rest of government to oppose it being ended because no doubt plenty of them are still at risk as well.