Its happened to us all. We get the changes back on a long document as a series of comments from the client and as we work our way through the changes and pieces get rewritten or extra copy gets inserted we soon find ourselves in the situation where the client has said something like “P38, 2nd para, change 'this' to 'that'”. But try as you might you can't find a 'this' on the 2nd paragraph of page 38 … because the changes made earlier mean the copy has since flowed on another page or two. And with a hundred more pages its only going to get worse.
Better to start with the last correction and work your way towards the front, that way everything makes sense as you come to it. Yes your amends may well cause the text on subsequent pages to reflow, but since you've already made those changes it won't cause any confusion.