Hi,
We are currently trying to re-create the scenario on our end so that we can get a better understanding of the challenges that you are having with OneNote. To better assist you, would it be possible for you to send us some screenshots of what you are facing when you try to delete the contents of a table in OneNote? You may also find this Link helpful in using and managing tables in Onenote.
We look forward to hearing from you again soon.