If you do not change instances of nodes or not totally refresh grid
you can use
flyGrid.Rows.Reset();
flyGrid.Invalidate();
If you need to totally refresh nodes (by replacing old node instances by new node instances (for example another class of node)) you need refresh nodes collection:
flyGrid.Rows.Reset();
flyGrid.Rows.RootNode = null;//or flyGrid.Rows.RootNode.Items.Clear() doesn't matter
flyGrid.Invalidate();