During the moving and renaming section in OnNotee one of the section disappears and becomes visible only through web interface with ".onetmp" in section name. Master section for this one could not be deleted anymore.
To fix this issue I do the following trick: click change location, drill down to the folder structure and manually rename folders at OneNote. Removing the postfix help to fix this issue.
It would be good to allow to do this a bit straightforward and fix enormous issues during the OneNote sync.