I have already answered your support ticket on the subject. For convenience I will paste my answer here as well.
By design RadFileExplorer does not allow its ROOT directories to be deleted or renamed. Are you able to actually delete the root folder? If so, could you please provide a sample project so we can examine the custom content provider.
If the problem is that the Delete button is enabled, I would recommend you to manually disable it when the selected folder is the root. For your convenience I have attached a demo project to this thread which shows the exact steps in order to do this. Could you please check it and let me know whether it fits your requirements?
the Telerik team