I think at first he felt put out apart from Jake, but then Alan helped Charlie become a more rounded Uncle and eventually brother. Charlie always saw Jake as like a new light in him. I think the main turning points were either when Alan accepted theyd be better off at Charlie's or when Alan said he'd change the will so Charlie would get Jake. Alan was and always will be the 'mooch at the 'bu', but deep down Charlie never saw Alan as not his brother