Local files are not backed up on your device or a backend server on our end and will be deleted if you delete the app.
Documents stored locally on your device live only in iAnnotate and are not backed up. These documents will be deleted if you delete iAnnotate from your device. The documents are also NOT backed up via iCloud device back up. You will need to back up any documents stored locally in iAnnotate to another device or cloud server.
If you want to back up documents via a cloud server look here for guidance on adding cloud connections in iAnnotate and here for information about transferring documents from one location to another.