We are not aware of such problem and you are the first one to report it. Do you experience this behavior using the standard functionality of RadFileExplorer? If you have implemented custom delete functionality, in order to be able to provide more to the point answer we will need to examine and debug the code locally. Could you please open a formal support ticket and provide fully runnable sample project reproducing the issue?
In addition, RadFileExplorer heavily relies on ASP.NET client callbacks, which do not work very good with the MS Ajax framework, and this may be causing incorrect folder loading.
the Telerik team