It is very easy to transfer your files from v3 to v4 and, once transferred, all of your annotations will still be there. If your files are saved to a cloud storage connection, like Dropbox, they'll be there when you create that same connection in iAnnotate 4.

If you have files saved to your Local Files, simply select them and choose the Send to v4 action. They'll then appear in your Local Files storage connection (once you add it) in iAnnotate 4.