How much does it cost to have the engine rebuilt on a 2013 Prius

Hello, first, I would appeal to Toyota for assistance, as the work is underway, and you appear to be at the mercy of the dealership. Also, in California, you have rights overseen by the Bureau of Automotive Repair regarding an estimate change like that. It seems kind of unacceptable that this estimate change occurred. But before that, it seems unreasonable that a 7 year old vehicle would be left without assistance by Toyota. Seek help with the service manager, general manager, or Toyota themselves. Most shops in the field are not equipped to "rebuild" an engine. You'll be installing a new or rebuilt engine block - short or long, not having the engine rebuilt for you.