Apple has created an ecosystem that allows for most iOS apps to automatically back up their data using iTunes or iCloud. iAnnotate is not compatible with either of these services right now. We are investigating the possibility of adding that capability in the future, but in the meantime, we strongly advise our users to use one of our four supported cloud services as your primary file storage solution. This will ensure that your documents are automatically backing up and the safety of your documents and annotations will be much more secure.
Keeping files in the cloud ensures that your changes are backed up whenever any document tab is closed, or when the sync button in the upper right corner of the app is pressed. It also allows you to access documents from other devices via those cloud services and enables you to easily transfer your work from one device to another.