What issue?
Let me try to make this easier for you.
When you put files in your "OneDrive", that is just a SharePoint Document library.The files will live inside that document library. If you want to sync those files down to your machine, then you would click the "Sync" button and it will start the "OneDrive
for Business Sync Client". That client will keep those files in sync on your machine.
When you sync those documents, you see the files in your windows explorer. There is also another copy of all your data in a folder you cannot see. This is called the Cache folder. So, if you have 10Gigs in the cloud, when you sync that library down to your
machine, you will have 10Gigs on your machine in the OneDrive for Business folder, and you will actually have another 10Gigs in the Cache folder.
So, now lets talk about OneNote.
When you sync a OneNote file down to your machine, you do NOT want it to create another cache copy on your machine. This can mess up your notebook and mess up the sync. You also do NOT need to sync this OneNote file with OneDrive for business.
The OneNote desktop app on your machine will be able to connect to any OneNote file, no matter where it is, and it will keep that file in sync. PLEASE LISTEN TO WHAT IM SAYING.. The "OneNote Desktop App" will keep the file in sync, no matter where it is.
So, you want to put the OneNote file in a Document library in SharePoint. You DO NOT want to sync that library down to your machine with OneDrive for Business.
You can open the OneNote file in your OneNote desktop app and it will stay in sync because the OneNote Desktop app is doing the syncing.
So, here are your steps
1. Login to the Office 365 portal,
2. Click on "OneDrive"
3. Click the gear on the top right, clcik on "Site Contents"
4. You can either use the "Site Assets" library or you can create a new document library. I use Site Assest.
5. Upload your OneNote file to this "Site Assest" library, or move it somehow.
6. Click on the OneNote file in the Browser, it will open up OneNote Web Client in the browser
7. Once its open in the browser, just click "Open in OneNote'
At this time, The file will open in OneNote Desktop app, and that link to that file will stay in Sync. So anytime you edit the OneNote Notebook, it will sync those changes up to the file online.
If you repeat this process with your other machines then you will be fine. Each machine will sync back to the cloud
I hope this is clear enough for you, if you have any other questions or need something else answers, just ask