I have the exact same issue except I am using FileSystem + Syncthing. In the initial sync everything passed from mobile to desktop. I just did a test notebook with a note inside of it on the phone to see that it syncs and it does. However from the desktop (also linux) only the notes within already existing notebooks in the Android phone are the ones that sync, in other words it doesn't create new folders from the Linux Desktop to the Android App.
I can tell syncthing is actually working and storing it because before this issue I was pretty much saving everything just in the phone but sharing it to a folder using syncthing, and all the data was restored when I imported it to the desktop from that same folder.