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For several years I've worked with a document and added lots of comments to it (teaching notes). Now there's a new version of the document from the publisher. Most pages are the same, but some have changed. I know I can print or download my comments, or manually copy and paste each one to the new document, but it's over 2,000 pages long. Is there a way to update the old document with the changed pages or merge my comments into the new document in the right places?
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You can use the Replace Pages command to maintain the comments in place. However, if the text moved around on the page the comments will be out of place after you do so, but it's still your best option.
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Will Replace Pages compare the documents to see what's the same and different on its own, then replace the ones that have changed, or will I need to check every page and decide manually?
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No. It will simply replace the pages you tell it to with the pages you tell it to. It performs no checks or comparisons of any kind. That's up to you.
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Replace pages preserves the comments while replacing the page contents (but backup carefully!)