How to flash arduino control board with her bootloader ?

Hi, i have problem with arduino robot control board. I was uploading program from simulink to the board like usually. After that there was a problem with connection and COM port. The computer was not able to recognize COM port of board. On forums i found the solution that I have to flash board with external programmer like UNO with ISP sketch. It was succesfull but in control board is motor board bootloader not control. Now i can´t upload program from simulink on target control board because of the incorrect bootlader. Is there any option how to flash the corrent bootloader on the control board ?

Thank you Andrej