"What's done is done" means that you can't change something. For example, if you break something that can't be fixed, you can sigh and say:
Oh well. What's done is done.
You could also say this if you bought something that you're not happy with but you can't return it.
When you say "what's done is done" it sounds like you're not very happy with the situation, but you're starting to calm down and accept it.