Do they have to return the Advance in this case? Is there any case where it makes sense fo reject the Advance?
You are right—if the carpenter just ran away, he would usually be sued. But in this specific case, the client (publisher) agreed to let him go. It’s more like: The carpenter said "I'm quitting to join the circus," and the client said, "Fine, keep the deposit, just leave."
In finance, we call this a "Write-off" to maintain relationships or avoid legal costs. It seems the publisher decided it wasn't worth fighting over.