Hello. I'm going to throw the new firmware into the board...

Hello.
I’m going to throw the new firmware into the board… PROCEDURE: I plug the usb cable into the board and pc. Easily connect it under COM3. Then put the boot connector on the boot connector and press the reset button. The board disconnected from the PC and changed to AT90USB1286 (no COM3 port anymore). I’m going to add a new firmware, but there is a problem that I can not see in COM3 port. So I do not want to load a board after reset but without resetting and unplugging the boot connector it’s all, and in arduine it’s the COM3 port.
Did anyone meet this problem?

I have printer PIRX… with board (Printrboard A based on printrboard) (Printrboard revf — I think this is my original board)
Thank you for advice.