Dear Chris DeSchepper,
Good day!!
As per the description shared, I understand your concern i.e., when you open the attached Excel spreadsheet from the OneDrive you will encounter an error message when the Excel is already opened, and I have tested the behavior at my end with the latest version of Semi-Annual channel by inserting the Excel spreadsheet via OneNote 365 app (Insert tab> Spreadsheet> Existing Spreadsheet> Attached as file).
When we open the attached file from the OneNote app when the inserted Excel spreadsheet is opened and Excel app is opened, the attached file is opened without any issue. In this situation, I suggest you perform Online Repair to the Office apps and check the outcome. Reference: https://support.microsoft.com/en-us/office/repair-an-office-application-7821d4b6-7c1d-4205-aa0e-a6b40c5bb88b
If the problem persists, can you please share the screenshot of the OneNote app Account page. Open the OneNote app> File> Account> Take a complete screenshot and share it with us.
Thanks for your patience and understanding.
Best Regards,