Hello Looby,
Welcome to Microsoft Community.
Generally speaking, when a file is synchronized to the cloud via Onedrive, the file will not be lost unless you manually modify the data in the cloud. Is the content displayed in OneDrive on the web page complete?
In addition, if convenient, could you please provide the screenshot information of the folder nested in the following folder so that I can check this? Because I'm sorry I didn't understand what you meant in the second paragraph.
What are your current requirements? Are local files not fully synced with the OneDrive cloud? Or are you worried about losing your files? Or some other concern?
If anything is unclear, please do not hesitate to let me know.
Best regards,
Mitchell - | Microsoft community support expert from MSFT