Found a solution:
private void flowLayoutPanel1_DragDrop(object sender, DragEventArgs e)
{
Control target = new Control();
target.Parent = sender as Control;
if (target != null)
{
int targetIndex = FindCSTIndex(target.Parent);
if (targetIndex != -1)
{
string cst_ctrl = typeof(CustomControl).FullName;
if (e.Data.GetDataPresent(cst_ctrl))
{
Button source = new Button();
source.Parent = e.Data.GetData(cst_ctrl) as CustomControl;
if (targetIndex != -1)
this.flowLayoutPanel1.Controls.SetChildIndex(source.Parent, targetIndex);
}
}
}
}