Dear Kenji1484,
Good day! Thank you for posting to Microsoft Community. We are happy to help you.
As per your description, it seems that you are having issue with OneNote Pen Ink, showing in different color when exporting to PDF.
If the understanding above is right, we've also done a quick test in OneNote within M365 in version 2308, and we cannot reproduce a similar situation on our side, below attached is the screenshot of our test for your reference:

Given this, to help you better, we would like to collect more detailed information you're experiencing so that we can have a further investigation:
- Are you using OneNote desktop app or OneNote online web app in browser? Will they encounter a similar situation?
- Will the same issue occur if you draw in other Office apps such as Word, and export to PDF?
- What about the other people in your organization, do they encounter the same situation as yours?
- Please also share a screenshot of the Office version as shown below by opening OneNote desktop app within M365 > File > Account

Welcome to post back when you have any update, we will continue doing best to assist you.
If the understanding above is not consistent with yours, please feel free to post back and point that.
Your understanding and patience will be highly appreciated. We hope that you are keeping safe and well!
Thanks for your cooperation.
Sincerely,
Rhoda | Microsoft Moderator