Νομίζω ότι πρέπει να κανείς override τη Serialize μέθοδο του CodeDomSerializer και να βάλεις εκεί τη λογική για υπάρχονται αλλά controls. 

https://stackoverflow.com/questions/4305140/how-to-use-designerserializerattribute-on-a-custom-user-control/4305495#4305495 

Private Sub Me_ParentChanged(sender As Object, e As EventArgs) Handles Me.ParentChanged
    Dim _ParentForm = DirectCast(Me.FindForm, Control)
    Dim _ControlName As String
    If _ParentForm IsNot Nothing Then
        For Each _Control As Control In _ParentForm.Controls
            If TypeOf _Control Is MyUserControl AndAlso _Control IsNot Me Then
                Throw New ArgumentOutOfRangeException("", "You can place only one " & _ControlName & " control per form.")
            End If
            _Control = _ParentForm.GetNextControl(_Control, True)
        Next
    End If
End Sub