How do you handle situations where you strongly disagree with an author's choices in their manuscript?

That depends on the context and why I disagree with them. I will often get emotionally involved in the stories I'm reading and the characters within them, and when authors do terrible things to them, as we love to do, I will often be upset and disagree with what they've decided to do, but I understand that this is the direction they want their story to take, and I respect that decision. I recently read multiple books, however, where there were situations involving minors that I felt did not need to be included in the stories the way the authors had included them in their stories. I included my thoughts in my feedback to the author, explaining that I understood the purpose of their decision, and why they'd written the scenes the way they had. I understood their intentions and how they wanted those scenes to play to the reader, and then I explained how they came across to me as a reader, which likely did not align with their intentions. Many of the authors came back to me after receiving the feedback to discuss the issue. Further, some made changes, and some may not have, which is, of course, their prerogative as the author. Something I say to every client of mine, at least once, is that my feedback is generally my opinion and not a hard and fast rule that should be followed. They know their story better than I do and where they want to see it in the future. My role is to help provide a critical outside view to help them decide how to move forward with that story.

When I strongly disagree with an author’s choices, I focus on offering constructive feedback while respecting their creative vision. I explain the impact of their choices on the reader, suggest alternatives if appropriate, and acknowledge the author’s intentions behind the decision. I aim to be honest but tactful, framing my concerns as opportunities for improvement rather than criticism. Ultimately, I respect the author’s right to make final decisions, understanding that their vision is key, and my role is to provide support, not impose my preferences.