The new MCU timeline breaks Agents of SHIELD's story and connection to the overarching franchise. When Marvel Television launched Agents of SHIELD in 2013, it was billed as the official MCU tie-in. In fact, the first two seasons dovetailed perfectly with the movies, reinforcing the sense everything was happening in a single shared universe. As Marvel frequently put it at the time, "It's all connected."
Of course, it was too good to last. Behind-the-scenes drama at Marvel ultimately led to a major corporate restructure in 2015, with Marvel Studios pulled out of the wider Marvel Entertainment group and placed under the leadership of Kevin Feige. The relationship between Marvel Studios and Marvel Television grew more distant, much to the frustration of actors such as Chloe Bennet. By 2018, Marvel Television had no idea what the films had planned, and so they quietly ignored Thanos' snap in Avengers: Infinity War - the biggest event in the history of the MCU, ignored by the tie-in TV series. In the end, after Agents of SHIELD season 7, viewers simply concluded the Marvel TV show is set in a different branch of the Multiverse. It was assumed the two timelines split apart at some point, perhaps as a result of season 5's time travel.
Sadly, even that idea looks to now be impossible. A new MCU timeline has actually adjusted the order of the Phase 1 movies, moving Thor: The Dark World to immediately after The Avengers. It makes sense, because this begins with the trial of Loki, but it has a significant impact on the order of events. It means that, in chronological order, Thor: The Dark World should now be considered as happening prior to Iron Man 3. Unfortunately, this blatantly contradicts Marvel's Agents of SHIELD, particularly the show's tie-ins with Iron Man 3 and the villain group AIM.
Agents of SHIELD season 1 begins with a plot in which Phil Coulson and his new team confront a Hydra cell who are working with a sample of Extremis. This was an unknown in the MCU until the events of Iron Man 3, and even SHIELD consider Extremis to be new, suggesting the show starts shortly after Tony Stark went toe-to-toe with the Mandarin. But as season 1 continues, it features a prominent tie-in with Thor: The Dark World, with Coulson literally sent to London to clear up the mess Thor left behind. At the time, this tie-in appeared to help provide a framework and structure to the MCU, giving a sense of the sequence of events. Now, thanks to this new MCU timeline, it is a major continuity problem.
There's no effective way of resolving it. The only conclusion can be that Marvel Studios is not interested in Agents of SHIELD, and the show has been consigned to a completely separate branch of the Multiverse. It was never happening in the same world as the movies at all, merely in one that initially resembled it, but ultimately went in a completely different direction. It's a heartbreaking conclusion for lovers of Agents of SHIELD; frankly, the show deserved better.