Can a paper get rejected after acceptance due to incorporation of reviewer comments Recently I got a paper accepted in a high impact journal. The acceptance letter came to me with a few reviewer comments, and it was recommended in the letter to take care of those comments. I submitted the final version with incorporating those revisions in the paper and due to one particular comment, I had to change a paragraph almost entirely. 

But now after the proofreading, the journal says only formatting changes can be made, and other changes need further approval from Editor in Chief. Can this anyway jeopardize the paper and result in its rejection? Also, is there any way to communicate with the journal to settle this issue?
What you've described sounds like a 'conditional acceptance', but I'm confused how you got to the proof stage without addressing the comments suggested. How did that happen? Also, no, do not make major changes during the proof stage.