Probably using the same way than programming 1000 FPGAs :

https://embdev.net/topic/447188#new

stupid man.

Elico C. wrote:
> After I finish the prototype design and compile on some ARDUINO
>  board , how do I move to mass production ?

I would consider using a naked µC instead of an Arduino board. Because 
is is typically much cheaper.

> Say how do I program 1000 chips with that scetch after it was compiled
> and tested on that ARDUINO board ?

The method you used for 1 board works for 1000 boards as well. It just 
takes more time.

If you decide for a naked µC on it's own board, you will probably have 
it manufactured by someone. Most board manufacturers also offer the 
service to flash a program of your choice.

As Microchip now sells the Atmel chip, you could buy preprogrammed chips
cheaply using microchipdirect.com .