Hi Jess,
Thanks for posting in the community, I’m glad to offer help.
First I’d like to explain that the embedded class notebook is created by “SharePoint App”, that’s why you can’t delete it in your OneDrive as you are not the owner.
In fact, every team is a SharePoint site, and all the contents including the embedded class notebook are stored in the corresponding site. You can go to File tab > Open in SharePoint > Site contents > Site assets to locate it, however, based on my test, we can’t delete it even I am a global admin who has the highest permission.
This seems to be a limitation, as a workaround, if the team that the class notebook belongs to doesn't store too much important files, the best solution is to create a new class team with a new embedded class notebook.
If you don’t want to leave that team for some reason, I’m afraid you might have to delete the contents of the class notebook manually as we are not allowed to delete the whole notebook directly.
I’m sorry for the inconvenience, in this case, I recommend you vote for the following idea or submit a new one in UserVoice, it is the best place to let the related team hear your needs, anyone’s suggestion could have a chance to be adopted by Microsoft, your understanding will be highly appreciated.
Reference:Delete Class Notebook
Hope the above information can give you some guidance and help you a little, please feel free to post back if you have any concerns.
Best Regards,
Arck