Magnetrons and Aether Extraction Explained (graphics)

In the movie "Avengers: Endgame," the extraction of the Aether was made easier because the Asgardian Asgardian king Thor, who had traveled to the past, had access to knowledge and resources that were not available during the "Thor: The Dark World."In "Thor: The Dark World," the Asgardians were not aware of the true nature of the Aether and did not know how to extract it safely. Additionally, the Dark Elves, led by Malekith, were actively trying to use the Aether for their own purposes, making the extraction process more difficult.In "Avengers: Endgame," Thor had access to the knowledge and resources of the Asgardians in the present, as well as the assistance of the Avengers. This allowed him to extract the Aether more easily and use it to defeat the villain Thanos.

The in-universe answer is that time has passed and knowledge has advanced

The Dark World takes place in 2013, while Endgame (at least, the time that Thor and Rocket travel from) is in 2023.

While this may not seem like much, this is definitely enough time for technology to evolve to achieve things previously thought impossible. This is especially true given that Rocket Raccoon, Tony Stark, and Bruce Banner were all on hand to work on a safe extraction method, armed with the knowledge of how things were resolved previously (the Asgardians at the time were unsure if Jane could survive extraction at all), as well as having as much time as they needed to perfect it, thanks to their upcoming time travel.

The simpler reason is plot convenience - the challenge of retrieving the Aether is not how they remove it from Jane, but rather taking it without being caught by her or the Asgardian guards. By handwaving an extraction device, we don’t need to worry about the plot discrepancy.

https://www.researchgate.net/publication/233814697_Secrets_of_the_Aether
(PDF) Secrets of the Aether - ResearchGate

Numerous predicted corrections to modern physics are revealed and within the realm of experimental verification. The latest version of Secrets of the Aether is ...