I have had this problem, too, but tonight I discovered something about how backups work, and the problem is resolved for me, at least for now.
I had wanted the planner to be synced to my iPhone so that I could refer to it easily when away from home without having to take the iPad with me everywhere I went, but the planners were not showing up. All the sticker sheets were there, and other notebooks I was working on, but not the planners.
Earlier this week, I got a new iPad, and I wanted to make sure the planners were syncing correctly so they would sync with the new iPad once I got it up and running. I used the settings on GoodNotes to do a manual backup of the planners to iCloud, having no idea how to restore them.
When I got the new planner and got GoodNotes up and running, it synced everything very quickly...except for those planner files. I had backups of the original planners, but had done a lot of work inthe originals and was not happy about the thought of redoing it.
Google to the rescue!
I googled syncing issues with GoodNotes, restoring backups, and anything else I could find.
The answer was in the GoodNotes forum. Manual backups are stored in a zip file. I have my GoodNotes set to back up to iCloud, so I checked iCloud drive on my PC, and sure enough the files were there.
It's super easy to restore them to GoodNotes..
So for me, I've at least temporarily solved the problem. Hopefully everything will continue syncing and these files will end up on the phone. If not, I can download the backup to the app on the phone just like I did on the iPad
Anyway, I hope this was helpful to any of you experiencing GoodNotes syncing issues, and I hope this works for you.