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Kanan and Ezra have already encountered Vader (along with Ashoka) so he's aware of two Jedi (or at least Force-users) working with the Rebellion. However, after the encounter on Malachor, Vader seems to forget all about them. At the least, he doesn't appear on-screen.

Why wouldn't Vader be chasing down potential Jedi threats? Does he have something better going on? Thrawn presumably would identify or at least suspect the use of the Force by his quarry, so why not consult with Vader?

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    I can't find new-canon sources as to what Vader is up to between the season 2 finale and Rogue One. This question might be unanswerable.
    – Daniel B
    Sep 13, 2017 at 6:27

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In the book Thrawn: Alliances (which is both canon and takes place after Rebels) it is clear that the Emperor expects Thrawn to deal with that rebel faction, as Thrawn promised he would.

[Thrawn had] already promised the Emperor that he would deal with Jarrus and the Phoenix rebels who had so recently escaped him... But Vader had no patience for failure of any sort, no matter what the reasons or excuses. For now, he was waiting; but he was more than ready to step in to solve that particular problem if the grand admiral failed.
- Thrawn: Alliances prologue

Later, in an exchange with Vader, Vader suggests that he will need to be the one deal with the rebels, but Thrawn assures Vader that he will find and defeat them.

"What about Atollen?" Vader countered. "You were unable to stop the rebels there. Now it will fall to me to find and destroy them.
"My war with the rebels is not yet over." Thrawn said softly. "I will defeat them."
"Good," Vader said. "Let us return to Coruscant, that your campaign may continue."
- Thrawn: Alliances ch. 17

Thrawn doesn't want Vader's help because among Palpatine's top leaders, there is always a struggle (or at least perceived struggle among some of the players) for the top spot.

Looking into Vader's thought process:

But he realized now that he had nothing to fear...No matter how high Thrawn rose in the ranks of the military, he would never have the necessary standing to challenge Vader's position at the Emperor's side.
- Thrawn: Alliances ch. 20

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