The consensus top farm system at this time last year, the Atlanta Braves have fallen behind the San Diego Padres due to the depth of the Padres and the graduation of a few Braves players to the major league level.
That does not mean, however, that the Atlanta Braves would not be in the conversation for the #2 system in the game, even with losing the prospects that were stripped from the team in November of 2017 along with the graduations to the majors in 2018. The recently-released MLB Pipeline end-of-season update to their top 100 rankings show exactly that.