Large OneNote Notebook Fails During Migration: Root Cause and Fix

When you migrate a large OneNote notebook to SharePoint or OneDrive for Business, the process may fail with a generic error or hang indefinitely. This usually happens because the notebook file exceeds the size limits or contains embedded files that the migration tool cannot process. In this article, you will learn why large notebooks fail during migration and how to fix the problem using specific steps and tools.

Why Large OneNote Notebooks Fail During Migration

The root cause of migration failure is the .one file format and the way OneNote stores content. A single notebook is a folder containing a .onetoc2 file and one or more section files with a .one extension. When the notebook is large, the .one file for a section can exceed 2 GB, which is the hard limit for OneNote sync. Migration tools such as the SharePoint Migration Tool (SPMT) or the Microsoft 365 Migration API also enforce this limit. If any section file exceeds 2 GB, the migration fails for that notebook.

Another common cause is embedded files within notebook pages. Users often attach PDFs, images, or Office documents directly into OneNote pages. These embedded files increase the size of the section .one file. If the total embedded file size plus the page content pushes the section over 2 GB, migration will fail.

A third cause is the presence of orphaned or corrupted section files. These files are not visible in the OneNote client but still exist inside the notebook folder. Migration tools attempt to process all files in the folder, including orphaned ones. If a corrupted file is encountered, the migration stops with an error.

Steps to Fix a Large OneNote Notebook Migration Failure

Before you start the migration again, you must reduce the notebook size to under the 2 GB limit per section. Follow these steps in order.

1. Check the notebook size in the OneNote desktop app
   Open the notebook in the OneNote desktop app. Go to File > Info > Settings > Notebook Size. This dialog shows the total size of the notebook and the size of each section. Write down which sections are larger than 1.5 GB. Those sections are at risk of causing migration failure.
2. Export oversized sections as separate notebooks
   For each section that exceeds 1.5 GB, right-click the section tab and select Move or Copy. Choose a new notebook location. This creates a separate notebook with that section only. The new notebook will be smaller and can be migrated independently.
3. Remove or compress embedded files
   Open each oversized section and look for attached files. Right-click an attached file and select Remove if it is not needed. For files that must stay, download them to a local folder and link to them from the page instead of embedding them. This reduces the section file size.
4. Use the OneNote Section Export feature
   If a section is still too large after removing files, export it as a single .one file. Go to File > Export. Choose Section and then OneNote 2010-2016 Section (one). Save the file to a local folder. This creates a clean .one file without orphaned data.
5. Delete orphaned section files from the notebook folder
   Navigate to the local folder where the notebook is stored. The default path is %userprofile%\Documents\OneNote Notebooks\. Open the notebook folder and look for .one files that do not appear in the OneNote app. Delete those files. Then run the OneNote app and verify the notebook opens correctly.
6. Run the SharePoint Migration Tool again
   Open the SharePoint Migration Tool. Select the source notebook folder and the destination SharePoint site. Before starting the migration, click Settings and enable Preserve file metadata and Preserve folder structure. Then start the migration. The tool will process each section file individually.

If SharePoint Migration Still Has Issues After the Main Fix

OneNote Notebook Migration Fails with Error 0x80004005

This error indicates a corrupted section file. Open the notebook in the OneNote desktop app and try to open each section. If a section fails to open, right-click it and select Delete. Then recreate the section from a backup or from a previously exported .one file. After removing the corrupted section, run the migration again.

OneNote Notebook Migration Fails with Error 0x80070002

This error means a file in the notebook folder is missing or has an invalid path. Check the folder structure in File Explorer. Ensure all .one files and the .onetoc2 file are present. If any file is missing, restore it from a backup. Then run the migration again.

OneNote Notebook Migration Hangs at 99 Percent

This usually happens when a large section file is being processed. The migration tool may appear stuck because it is trying to compress the file. Wait at least 30 minutes. If the progress does not change, cancel the migration and split the largest section into multiple smaller sections. Then restart the migration.

OneNote Notebook Migration Options: SPMT vs Manual Upload

Item	SharePoint Migration Tool (SPMT)	Manual Upload via OneNote App
Best for	Multiple notebooks or large folders	Single small notebook under 500 MB
Speed	Fast, uses parallel processing	Slow, depends on upload bandwidth
Error handling	Logs errors and continues	Stops on first error
File size limit	2 GB per section	2 GB per section

If you use the manual method, open the notebook in the OneNote desktop app and go to File > Share > Move to OneDrive. This method works only if the notebook is under 2 GB total. For larger notebooks, use SPMT.

After you complete the migration, open the notebook in the OneNote for Windows 10 app or the browser version to verify all sections are present. If you split sections into separate notebooks, you can merge them back together after migration by moving pages between notebooks.

As an advanced tip, run the OneNote Team Notebook Analyzer tool before migration. This free tool scans the notebook for corrupted sections, orphaned files, and size issues. Fix all reported issues before starting the migration to avoid failures.