Lmfao, those exact things happen after she defeats them, this is the full quote:
The secret manipulations of the Sith Triumvirate following the Jedi Civil War almost destroyed the Republic. With infrastructure crumbling and the Jedi Order nearly extinct--its Masters almost entirely slain, and its younger members slowly emerging from hiding--the future seemed bleak. But the Jedi Exile and the other heroes of the Jedi Civil War would not see the Republic fall.With renewed treaties and alliances, trade gradually began to flow and the Republic military regained its strength. Meanwhile, the Exile trained new Jedi recruits, forming a council of her companions who achieved mastery and welcoming others who came out of hiding. After years of slow but steady growth, the reborn Jedi Order made a triumphant return to its long-abandoned temple on Coruscant.
But the Jedi Exile could not forget Darth Traya's final warning, suggesting that evil remained in the Unknown Regions. With the Jedi Order flourishing, the Exile left the known galaxy to follow her former commander Revan into darkness.
The novel AP. You said TOR and the novel showed it to be wrong, despite the fact that in the novel and TOR, Surik did not completely reform the Jedi. Stop dodging. In the novel, Revan's son with Bastila is toddler and the Jedi are hardly "flourishing." This is why I said you are cherrypicking sources, just taking the parts that sound good and completely ignoring the parts of these sources that contradict each other.
Except the actual plothole was created by the novel itself. The Order was wiped out, all Masters dead or arrested. But we get to the novel and it's as if the Dark wars never occurred. We never get a real timetable of when Meetra's part in the novel actually starts, but we know it's years after Revan is captured and jailed. The companions are stated multiple times in the game to be the new generation of Jedi.
"They were the true lost Jedi, you know; the ones on which the future will be built."
- Kreia
Beyond that, we have Brianna becoming the Jedi historian, Mical becoming one of the heads of the High Council, Mira dying to save a colony. Them becoming the new Council along with others they welcomed out of hiding, is far from hard to believe when Traya's visions of their future are exceedingly malleable.