How to Reset milli() function?

The Arduino IDE does not send a 'reset' when the serial monitor port is opened. However in the Arduino 0009 and later compatible hardware DTR (or RTS on boards made for the FTDI TTL-232R cable) gets asserted when the serial port is opened and a hardware reset is generated.

So, on the one hand, you are right in that a reset IS generated, BUT, on the other hand, you are wrong, because it IS NOT generated by the Arduino IDE.

I hope this helps make it clear.

cheers ... BBR