We are sorry about it. GoodNotes 3 has been discontinued and is only supported on iOS 7 or below because iOS 8 is not backward compatible with iOS 6 apps. The backup all process should still work to let you migrate all documents to the new GoodNotes 4 which is a paid upgrade and added many new features like iCloud sync, handwriting search and iPhone support. Please follow the instructions in this article to migrate your documents.
GoodNotes 3 was written for iOS 6 and we didn't know what would be changed in later iOS updates. It would require a significant amount of time to make it compatible with current iOS version and we don't have the resource to do it.