stopping sketch (loop) and ejecting arduino board in linux

Hi

On my laptop, I have the ide setup on linux with a sketch running on a connected arduino board. Do I need to stop the loop and eject the board before removing it? Within the loop, there is a Serial.print and Serial.flush going on.

My arduino board is a clone : ArduPilot Mega as seen here:
http://code.google.com/p/ardupilot-mega/wiki/Hardware

and here:

Besides being plugged into the pc for programming with the IDE I have a separate power supply (wall wart) running to it (as described here Google Code Archive - Long-term storage for Google Code Project Hosting.).

Thanks...

No, you don't.