Carla is correct. Even after saving, the annotations can be deleted while the document is in Paperport. Once it is imported into the chart however, the changes are "permanent". Even with Adobe, I know of no completely secure way to markup a document. I can take an Adobe document from AC, print it to Paperport, mark it up and reimport it back to AC. It would then have to be signed off again by me and the original deleted but if I were the one with criminal/unethical intent, too bad. So, I think there will be security issues in any program.
Leslie