Hi. I don't think there's any similarity between one user editing one note on two devices, and someone making a major revision in the architecture of the account - though the underlying cause is pretty much the same thing.
What's shown and stored on your local device is also synced to the cloud, and if you are making major changes, it will take some time for that to synchronise correctly.
You're moving dozens or hundreds of notes around and the server is trying to play catchup. It would have been a good idea to carry out any changes over a period, or leave the account overnight.
Sadly, trying to change what appeared to be happening mid way and reinstalling the app will probably only have made things worse. If you keep a regular backup of your account, now might be a time to see whether you can recreate what it looked like yesterday. If you don't have a backup I can only suggest that you log out overnight and log back in tomorrow to see where the account was left.
You may have to contemplate a manual repair to complete your reorganisation...