We were noticing OneNote Sync issues with SharePoint 2010 and below workaround worked for us,
1. Right-click section in question, Move or Copy...
2. Select another Notebook beside the one it resides in, Move.
3. Sync the changes.
4. Move the section back to the desired Notebook.
5. Sync the changes.
WOW - thanks spent some time with difficult sharepoint solutions. This worked in 2 minutes
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