You can have workflow apply those annotations for you based on a certain condition or you can just run the workflow manually. If you're referring to highlights or freehand annotations then it's going to be more tricky and you're probably going to need to leverage the SDK in order to copy those annotations over. It's hard to say for certain since I don't know what process you're trying to expedite here. You can maybe even leverage Quick Fields if you're redacting sensitive information or something along those lines.