i Believe possible reason is to this error is if you have multiple microsoft/o365 accounts, OneNote internally maps URLs to an account. The above error occurs if the account mapped to does not have access to that site. To fix it, follow these steps:

1.     Close OneNote (close and reopen notebooks in OneNote)

2.     open regedit (Windows+R > type "regedit" > press ENTER)

3.     navigate to Computer\HKEY_CURRENT_USER\Software\Microsoft\Office\16.0\Common\Identity\DocToIdMapping (you can copy/paste this link directly into the addressbar on the top of regedit)

4.     press CTRL+F to search for the unique domain part as it appears in the browser (ie. "mycompanyname" in "https://mycompanyname.sharepoint.com")

5.     make sure any reference to this domain is only linked to one account

Hi, thank you for that suggestion, but it didn't fix my issue.

However, reading the steps, I'm guessing the Error code: 0xE401069D c12qc, is related to conflict from different accounts.

I looked at the signed account area and realized that OneNote did signed in with all different accounts I signed in using the Edge browser.

I NEVER signed in with those account in OneNote.

I sign off from all those accounts from OneNotes, and the sync worked again.

Thank you for the starting clue, but would have been much more efficient if the error codes were documented somewhere.

PS: 

In Edge, I sign in again with different other accounts, and those are sign in, in OneNotes as well.

There is no mention of these behind the curtain behavior between Edge and OneNotes.

Looks like, starting now, I'll keep myself away from Edge.

As I mentioned before you might you have multiple Microsoft/o365 accounts, OneNote internally maps URLs to an account. From the edge browser you login to multiple accounts this could lead to this error.