The easiest way to make a non-cloud backup of your files, or to bulk transfer files/folders to your Mac/PC, is with the "Send to iTunes" command. You must be running iTunes v9.1 or later on your Mac/PC to utilize this feature. It's also important to note that once files are transferred to iTunes, they must then be moved to a permanent location on your computer.
In Document View, tap the document tab and select "Share..." > "Send to iTunes."
In the Library, iAnnotate features two options for accessing the "Send to iTunes" command:
Tap and hold on an individual file or folder and select "Send to iTunes" from the popup menu that appears.
Or, select multiple files/folders in your Library via their selection circles, then tap "Send to iTunes" in the Library Actions panel.
After pressing "Send to iTunes", the selected document or folder is sent to the desktop Mac/PC iTunes app currently using the same Apple ID as your iPad. Be sure to wait for the "Document Updates Complete" notification to ensure the transfer has finished. The larger the files/folders being transferred, the longer amount of time this procedure will take to complete.
To access these transferred files, connect your iPad to your computer and open iTunes. In iTunes 11, click on the iPad icon in the upper-left then click Apps on the left. Scroll down to locate the "File Sharing" heading. Select iAnnotate 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 transmitted via the "Send to iTunes" command. After selecting a document or folder, you can 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. You need to drag them from the File Sharing section to a folder on your computer.