We weren't able to see sub folders created in sharepoint the previous day so moved files to a sub folder we could see.
Those files aren't appearing in Power BI desktop, we can see them in PowerBI.com.
From your description, it seems you use SharePoint Folder data source in Power BI desktop to get data, but after you enter the SharePoint site URL and specify credential, the subfolder is not listed in retrieved data, right?
As you mention the subfolder is available on Power BI service, please ensure the SharePoint site URL and credential are the same both in desktop and service.
Best Regards,Qiuyun Yu