ATmega 2560 Firmware

Hello
I have what might be a silly question.
I have purchased a APM 2.5 board to start a Arducopter project.
In anticipation and prepping it's arrival I downloaded Mission Planner.
Once the program installed I clicked on a few of the setup steps to see the actual program instead of canceling and going around them. One of those steps was loading the Mission planner firmware.
What I didn't think about was I had my Mega2560 R3 hooked up at the time because I was working on another project.
Mission planner loaded the firmware onto the Arduino board because I clicked yes to load with out thinking I actually had a board on Com port.

The question is: does the firmware that Mission planner loads on the Mega stay in memory and possible effect sketches I load to the board in the future?
I have loaded a couple of sketches since the firmware was loaded and they seemed to work OK but I've noticed pin13 led flashing a steady pulse on one of the sketches that did not use pin13 as output or have a serial read.

Thanks in advance

As long as they don't touch the bootloader it shouldn't matter what is programmed into the chip, the next program will overwrite it.


Rob

Thanks for the response Rob

I figured that was the case.
Guess I'm just worried about the day I really do mess up the Mega. :blush:
Thanks again