This is probably hitting the SharePoint 5000 item list view limit. I’m not that familiar with the internals of the Microsoft product offerings, but If you’re not using Microsoft SharePoint v2, you could try that instead.
‘No files were found at the remote location’ using Onedrive for business has some discussion, and in this case switching to “v2” version helped. I’m not sure it will always. Logic and usecase for remote subfolders would be the long-term solution, but isn’t done yet. Meanwhile, large remote volume size is a workaround.