I am trying to figure out the best way (or any way) to compare and merge two PDFs. I have two versions of a document - one is clean, and the other is a working copy with comments on it. These documents are frequently updated, with new pages being added in. The pages that are added are sometimes added at the beginning or the end, but sometimes they are scattered throughout the document. It is important to have one clean copy and the separate one with the comments. I cannot figure out a good way to update them each without having to insert the pages individually on each document. What I am trying to do is to be able to update the clean version, adding in the pages where I need to, and find some way for Adobe to add the new pages into the working copy. I can perform the Compare Documents feature and be able to identify the pages that were added, but I cannot figure out how to get those added pages into the working copy automatically, while still retaining the comments in the working copy. The documents are hundreds, and sometimes thousands of pages, and the pages that are added are sometimes a few pages in one section, and sometimes a few pages here and there throughout the whole document, which is time consuming to add to one document, not to mention to a second.
I don't think there's a built-in way of doing it. It might be possible using a third-party plugin or script, but it's not going to be a simple task.