It's when you reset the ECU in the car. Usually the best thing to do after installing new intake equipment (short ram or cold air). Basically the car will retrain itself to handle the increase of air it's getting. Good way to get the most performance out of your aftermarket air filter. Although im not sure about this but I have heard that flashing the computer can void your warranty, but like I said, Im not sure.
Are you talking about flashing the ECU or resetting the ECU?
Those are 2 different things. Resetting just means you disconnect the battery for 10 minutes and then reconnect to wipe out the ECU's learned settings.
Reflashing the ECU will actually change the programming on the ECU by taking the computer out and reprogramming it with something completely new.
I used to flash program EPROMs at work just not car computers, but same concept.
Intake, you will need to reset the ECU to get rid of the CEL that will appear after the intake is installed. You don't have to reset it though. The ECU CONSTANTLY adapts to chages made. When installing intake be sure you research on which ones do NOT effect the MAF sensor. Some intake can sneak air past the ECU without being accounted for, making you run leaner and cause some tooning problems.