The easiest way to delete contents of an IsolatedStorageFile is to open it in the Truncate mode:
IsolatedStorageFile isoStore = IsolatedStorageFile.GetUserStoreForAssembly();
IsolatedStorageFileStream isoFile = new IsolatedStorageFileStream(myFileName, FileMode.Truncate, isoStore);
According to the MSDN , if a file is opened in the Truncate mode its size should be 0 bytes.