If you wish to keep all of your documents stored only on the iPad (in the Local Files folder) and not within any cloud services, then it is very important to make regular backups. This approach is generally more time-consuming and less efficient than keeping your documents backed up to a cloud service; as such, we only recommend it if you are handling sensitive and secure documents that cannot be stored in the cloud.
Please note: Automatic/full iTunes backups will not, under most circumstances, preserve your documents nor your annotations. Accordingly, it is recommended to make a manual iTunes backup instead, as described below.
Send to iTunes
The easiest way to make a non-cloud backup is to do so manually, via iTunes. You must be running iTunes v9.1 or later on your Mac/PC to utilize this feature. In the Library, iAnnotate PDF features a popup menu command that lets you send a document or folder to the desktop Mac/PC iTunes app. To use it, tap and hold any document or folder in the library, then tap the Send to iTunes button in the popup menu.
After pressing the button, the selected document or folder is sent to the desktop iTunes app that currently uses the same Apple ID as your iPad. In iTunes, click on the iPad icon in the upper-right then click Apps in the bar on the left. Scroll down to locate the File Sharing heading. Select iAnnotate PDF from the left column to display a list of transferred documents at the right.
iTunes does not list your entire iAnnotate Library contents here; It only lists those documents and folders that you have manually transferred via the Send to iTunes button. After selecting a document or folder, click "Save to..." to save it to any location on your computer.
*Please note: If you are using Send to iTunes to back up your work prior to uninstalling the app, you must save the transferred files/folders to your computer or cloud connection to avoid losing them when the app is deleted.
See here for more detailed instructions on the Send to iTunes process.