Starting with a detail I appreciated, I was surprised to see the third episode refer to the eventual Separatist capital as Raxus Secundus rather than just Raxus like in all of the previous shows. The relationship between the Raxus seen in the shows and the Raxus Prime junkworld seen in other media like the 2002 The Clone Wars game and The Force Unleashed always seemed to be something retroactively assigned by the books and not something that would ever be acknowledged in the shows, with the Secundus designation having been created well after the fact by Jason Fry. In general, I thought the Dooku episodes slotted themselves into the larger story very well in both details and larger themes.
I have seen some comments expressing doubt that it lines up with their ages for Mace to have been working with Dooku as he does in the third episode and for Mace to have joined the Council before Dooku did. Dooku: Jedi Lost‘s script estimated that Dooku was in his sixties when he served on the Jedi Council after Qui-Gon’s knighting, which would start roughly around 42 BBY, the same year Dooku left the Order. Legends precedent going back to The New Essential Guide to Characters stated that Mace was promoted to the council at the surprisingly young age of 28, which would be in 44 BBY. Neither of those two dates are currently set in stone but the idea that Mace and Dooku were peers in that regard despite the difference in their ages and Mace would be the first promoted is completely plausible based on what we already knew. The episode could take place in 44 BBY and still leave two years for Dooku to be promoted to the council before deciding to leave the Order as depicted in the audio.
One of the most common problems I’ve seen people have is the idea that the fourth episode wholly contradicts Master & Apprentice and Dooku: Jedi Lost by showing Dooku to still be part of the Jedi during The Phantom Menace when those stories depicted his exit years earlier. The episode never actually outright states Dooku is still a Jedi during this time despite him visiting the Temple, and there are some bits (such as Dooku needing Sifo-Dyas’ override to erase Kamino and Dooku not having met Obi-Wan yet) that imply he is in fact not still with the Order. Padawan recently set up this idea nicely by firmly establishing that Dooku did still regularly visit the Temple after his departure, a piece of information I imagine was likely put into the book just to preempt the questions they knew would be raised by the episode.
The biggest piece of information we had on Yaddle’s fate before the series was from The Visual Encyclopedia, stating that Yaddle elected to take a less active role in Jedi affairs and resigned from the council after the incident on Naboo. Despite the series showing her death in the days after Naboo, I thought it was cute that this still remains technically accurate, since Yaddle says in the series that she had already resigned from the council because of Qui-Gon’s death. I don’t know whether the decision for Yaddle to speak normally was made for The High Republic or for this show first but either way it is likely by design that the two stayed consistent because all previous precedent was for her to speak in the same manner as Yoda, even as recently as in LEGO Star Wars: The Skywalker Saga, which probably had to make a decision well before either of the others.
The fifth episode shows Caleb Dume with Depa Billaba in a story implied to take place near the very beginning of the war, despite the Kanan comic explicitly placing his apprenticeship to her in the war’s final months. This can probably just be chalked up to the two of them knowing each other a little before the comic’s events; though the comic implies they weren’t very familiar with each other until after Depa emerged from her coma years later, it also never definitively shows them meeting for the first time.
The continuity elephant in the room comes from episode six of the series, which seemingly depicts a different version of the events behind Ahsoka joining Bail’s rebellion than the version shown in the Ahsoka novel. I don’t generally have a problem with two stories showing two differing versions of the same event (I don’t mind the differences between the Kanan comic and the premiere of The Bad Batch much) but there’s no arguing that the one in the show diverges in ways large enough that make it hard to reconcile. While it does strain belief that Ahsoka would go through something that similar twice, I think making the two different events entirely might be a valid option, but I leave that decision to those who get paid to make it. In the big picture, the events are more or less the same: Ahsoka hides on a farming planet under the name Ashla until an Inquisitor arrives to raze the planet to find her, with her defeating him in single combat and leaving the planet to join Bail’s rebellion.
I think most of the differences are more superficial; Ahsoka can still purify the red crystals offscreen, and Sixth Brother having multiple masks is easier for me to swallow than an entirely different new Inquisitor when there aren’t really many unused designations left. The biggest problem I have is the exclusion of important players like the Larte sisters from the book with no room left for them to have been a part of it in the show’s version. It’s valid to be disappointed by that, particularly with the representation those characters brought, and no matter how they do it I hope future decisions to reconcile the two stories find a way to preserve them.