I don't know if this is an issue or used in part of a feature I am not aware of, but I ran into this problem when I decided to rename a notebook and gave it a "- " (that's a dash and a space) to force it to be at the top of the list.
Suddenly the notebook lost the ability to sync properly. Out of curiosity I tried the same thing with a note, and the same thing happened. It stopped syncing.
If this is a bug, let me know and I will start a topic on GitHub. Also, are there better ways to keep a note or a notebook at the top of the list?
I had a notebook named "new" I had been using for a few days. I renamed the notebook "- new" and synced. I thought all was fine and dandy until I tried to access it from another workstation. The other workstation did not reflect the change.
After playing with it for a while I couldn't get the two workstations to sync this folder, even after renaming it back to "new" on the original workstation. This persisted through rebooting the first workstation and restarting Joplin on the second workstation.
I even tried creating a note named "new". Went through renaming it to "- new" and the same things happened and posted my query.
Eventually I just made a new notebook ".New" and transferred the notes over. Everything has been working.
Since you had mentioned that it worked without problems I just went through the same exercise. Created a new notebook called "new". Renamed it as "- new" etc. Now I cannot reproduce the problem.
I have no idea what to say. It works for me as expected.