If your files are saved to a cloud storage connection, like Google Drive, they'll be there when you create that same connection in iAnnotate on your new device. If they're saved to Local Files, you'll want to use iTunes File Sharing. To use it, follow these steps:

Here are the 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. "send to iTunes"
4. Connect your iPad/phone to the computer with a cable, like you would to sync the devices. 
5. Now from the computer: select the finder icon
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 them to the desired location.