If I understand, and I probably don’t, the idea that the clones have chips in their heads will be removed?
That’s one example of things that make TCW feel incongruous to me, as the films characterize them as being genetically engineered to obey orders without question and be inhumanly docile. The Kaminoian prime minister in AOTC didn’t say, “We placed chips in their heads to make them more docile than the original host.”
Without wanting to spoil it for you, the episodes that expand on the obedience of the clones are generally considered to be particularly decent. They do reveal a new technical layer to that obedience, but I don’t know of anything featured in the episodes which is considered breaking established understanding.
The show does introduce new layers - or new interpretations - to established events. And obviously for any viewer there’s a chance that the retro-changes will conflict with their personal interpretation. However, one of the widely agreed on strengths of Clone Wars is the emotional resonance of the consequences of a lot of these additions.
To pick an example which isn’t too spoilery: You may have an initial hesitation when you hear that Obi-Wan had a romantic interest before episode 2. You might become more comfortable when it’s clarified that she loved him, but as a Jedi, he knew he couldn’t return that love. But you may still feel like this addition doesn’t belong. But the payoff for that new element is beautiful - I think that once you saw it you’d agree it was worth it.
Edit: To be more specific about answering your question, I’m not certain about that particular storyline. The addition doesn’t add much story value, and while it has some great moments it does have weak parts. It is referenced later in an important way, so I need to take a closer look at how all those elements play together. I’m tending towards downplaying the clone elements in my quality cut, or at least not treating them as mandatory.