We improved the sync performance in our latest update 5.3.17 for iOS/iPadOS and Mac. If one of your devices that you're using GoodNotes on has an older version installed, you may see the following error message: "App version out of date. Please upgrade to the latest version"
Install the latest update from the App Store and Mac App Store (v5.3.17) on all your devices which have GoodNotes 5 installed and sync with the same iCloud account. It should fix that error message with iCloud sync. In case your documents are still not syncing properly, restart your device to reset the iCloud Daemon should help.