Some users would suggest just changing the sync target in the configuration to move to another provider, but I would not personally recommend to do this because doing so is more prone to issues than starting a clean slate. The safest way is to make a full jex backup of all your note data, create a new profile in Joplin, import the jex backup, then set up sync to your new (empty) sync target. That way your data on Nexcloud and your data on OneDrive are not linked together in any way.
Regarding Joplin creating a second folder on OneDrive, that is the OneDrive bug that I mentioned (OneDrive tells Joplin the folder that it is allowed to access, and may randomly tell it to use a new folder). In usual circumstances this would not happen when you set up a new device using the same Microsoft account. If it happens then you will get the error "Fail-safe: Sync was interrupted to prevent data loss, because the sync target is empty or damaged. To override this behaviour disable the fail-safe in the sync settings.". That would block anything from being deleted, but you will need to basically back up your data and then delete everything from all clients and OneDrive and set up everything again, if that happens.