We constantly improve the sync performance for the app on iOS/iPadOS and macOS, so if one of your devices has an older GoodNotes version installed with outdated iCloud sync schema version, you may see the following error message like this one:
Install the latest update from the App Store on ALL your devices that sync with the same iCloud account. If you instead search for "GoodNotes 5" via the App Store app, it might show the Open button next to "GoodNotes 5" in the search results, making you think there's no new GoodNotes update. To be sure, ignore the button and tap on the app name instead, and see if you now see the Update button.
In case your documents are still not syncing properly, restarting your device to reset the iCloud Daemon should help.