When you upload a new model/code to an Arduino, it completely erases the previous code on the Arduino.
So you can make changes to your Simulink model and rebuild it again or build a new model onto the Arduino. The previous program on the Arduino will be erased.
For more information -
https://www.mathworks.com/help/supportpkg/arduino/ug/stop-or-restart-a-model-on-the-arduino-hardware.html