The best way to move files out of iAnnotate PDF (v3) is to use the "send to Tunes" and connect your device with v3 to a computer.
Follow these steps to move files out of version 3:
1. Tap the files/folders you would like to move (so that a check appears in the circle)
2. Tap "actions"
3. Tap "send to iTunes"
4. Connect your iPad/phone to the computer with a cable, like you would to sync the devices.
5. From a Mac computer: select the finder icon (File viewer in PC)
6. Find your device on the left side and select it.
7. Select "files" then "iAnnotate PDF"
8. Select the files you wish to save and move by dragging them to the desired folder location.