Jedi Conspiracy Kept The Shadow's Existence A Secret
According to the eighth Acolyte episode, Vernestra Rwoh, one Jedi in particular had overwhelming proof of the Sith's return. Vernestra knew far more about Osha, Mae, Brendok, and the Stranger than any other living Jedi once Osha killed Sol. Vernestra also seemed to have a past with the Stranger since she identified him via the Force upon arriving on Brendok and might have even known his actual name. She should, all things considered, have put together that the Sith had returned, or at least that someone quite strong in the dark side was active in the galaxy.
Although Vernestra was aware of the Sith's comeback, that knowledge does not really retcon The Phantom Menace given her actions. Vern's scenes in The Acolyte established that the Galactic Senate was pushing the Jedi toward more openness. Vern had already decided to keep Mae's murder under wraps, thus she had to intensify in the climax. The eighth Acolyte episode revealed that Vernestra covered up the Sith's return to the Council by framing Sol for Mae's murders rather than reporting the Sith's attendance.
Vern essentially framed Sol and covered proof of the Sith since she wanted the Jedi to appear bad before the Senate. This probably went beyond simple ego issues. From the catastrophe on Brendok to the return of the Sith, all the evidence Vern hid would have given Senator Rayencourt plenty of ammo to attack the Order with. She seemed to have a resentment against the Jedi. In any case, though, Verenstra Rwoh's actions kept the Jedi from knowing the Sith's complete return under awareness and prepared the ground for Darth Sidious to surprise the whole Order.
Yoda Aware Of The Conspiracy... But Were Other Councillors?
Yoda made a cameo at the end of The Acolyte episode 8; it appears that Vernestra informed him about her plot to conceal the Sith's return. Again, though, Yoda's awareness of the Sith's return does not inevitably retcon The Phantom Menace. Yoda very well could have done with the Stranger; he has hidden knowledge from the Jedi in the past, including when he kept the Nameless out of the Jedi Archives. Yoda also seemed far more receptive to the concept of the Sith's comeback in The Phantom Menace, which today would seem to indicate that he knew more than the other council members.
The eighth Acolyte episode showed Yoda knew the Sith would be returning. He might not have been the only Jedi Council member that knew though. Many of the Council members instantly discounted Qui-Gon Jinn's suggestion when he first informed them he thought the Sith had returned. But in their next conference, the Council was far more ready to believe him; Mace Windu even called Qui-Gon's concept the "mystery of the Sith." Now that The Acolyte revealed Yoda knew the Sith had returned, he might have informed the rest of the Council about Vernestra's plot without letting Qui-Gon know.
Should Star Wars choose to notify the Council of the Sith's comeback in The Phantom Menace, it would align with some of the intriguing prequel trilogy motifs. The franchise has already shown that the fall of the Jedi Order resulted from their own errors; Yoda's knowledge of the Sith in The Acolyte would make that even more common. Should Vernestra or Yoda have informed the rest of the Jedi about the Sith's comeback, they could have been ready, and Palpatine would have had a far more difficult access into the Galactic Senate.
The Acolyte hasn't finished outlining this.
Although Vernestra's conspiracy seems to help to explain why the Jedi still thought the Sith to be extinct in The Phantom Menace, there is obviously still much more narrative to uncover. Now knowing the Stranger was her former Padawan, Vernestra has Mae's aid in locating him. Though it hasn't yet been verified, The Acolyte season 2 will most likely follow Vern and Mae in their hunt for the Stranger and Osha. That research will probably provide Vern, and hence the Jedi, even more knowledge about the Sith and help to clarify how the Jedi neglected the Sith even more specifically.
The knowledge of the Sith that the ending of The Acolyte season 1 failed to address still begs some questions regarding the Jedi. Nothing Vernestra knew about the Stranger, for example, would explain why the Jedi knew about the Sith Rule of Two—which Yoda mentioned at the conclusion of The Phantom Menace. The Stranger's fate was also not revealed in the finale; with the cameo of the Darth Plagueis in The Acolyte episode 8, the Jedi still runs a rather high risk of learning the real power of the Sith.
Should it be renewed, The Acolyte season 2 will have an opportunity to tie off those unresolved issues and offer a flawless transition from the High Republic to the prequel trilogy. Given the number of viewers The Acolyte attracted and showrunner Leslye Headland's hints regarding The Acolyte season 2, it seems likely that The Acolyte season 2 will air. The Acolyte set up the tragedy of the Star Wars prequel trilogy rather well and offers a rather clear justification of how the Sith stayed hidden even if it does not get renewed.