We are using CRM 2015 Online.
We have custom code that creates SharePoint folders when we create Account records.

Here I created the account "TestSharePointOneNote001". This generates a SharePoint document location through our plugin. We can verify that in our SharePoint site:

And opening the folder up, we can see our folder structure (defined in our custom code, but just goes to show that it's still correct at this point in time):

But here is where it got tricky. We decided we are going to integrate OneNote aswell - and when we click the OneNote tab of the Activities section, this is what happens :

Refreshing the form and clicking OneNote once more gives another message:

If we go and look in SharePoint after doing this we notice that the SharePoint folder has changed into just a OneNote file..

Please, if anyone has any suggestions how we could get these OneNote files to be placed inside the "Accounts\*Account Name* " folder instead of replacing it, I would appreciate it!