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Hi SebastianCoV,
If you want to make sure your files are synced up, you can try navigating to File > Info > View sync status then click sync all. Because different issues can occur from time to time during syncing, I guess sometimes OneDrive mistakenly thinking your old files to be the newer ones. It's also good practice to back up locally, since if OneDrive is the only space to store your data, when any network or server issue occurs, you lose everything.
And to be clearer of your first question, I would like to ask:
- Which version of OneNote are you using on desktop now, OneNote for Windows 10, 2016, or etc.
- What do you mean by "open the prompt back up", can you share us some screenshots or more details.
A common method for fixing Office is to use the integrated repair tool, sometimes it helps, sometimes it doesn't.
Best Regards,
Thomas Lu - MSFT | Microsoft Community Support Specialist