We improved the sync performance in our latest update for iOS/iPadOS and macOS. If one of your devices has an older GoodNotes version installed, you may see the following error message:
Install the latest update from the App Store on all your devices that sync with the same iCloud account. It should fix that error message with iCloud sync. In case your documents are still not syncing properly, restarting your device to reset the iCloud Daemon should help.