This is expected behavior of RadFileExplorer. It is caused due to the fact that the deleted folder content is cached by the browser and when you navigate to the newly created folder with the same name this cached information is used. Caching of the folders content is used to increase the performance of the control.
I have logged this issue in our ToDo list and we will do our best to handle this scenario for one of our upcoming releases. Here you can find the PITS Issue: Public URL
At present, I am unable to provide a suitable workaround for this behavior.
the Telerik team