IAM (ignition advance multiplier) needs to climb back up to 1.0 (or 16). When you reset the ECU, the IAM value goes to 0, or whatever your map has for a min limit. Throttle will feel way less responsive because the ECU pulls throttle response, runs flat timing, and pulls boost until it feels "happy" with your new flash. Once it recognizes that your shiat isn't detonating just idling and normal driving, it climbs back up to 1.0 and you get 100% of the power. Some cars climb back up after a two mile drive, others can take a day of normal driving around. From there, the ECU learns and adjusts based on closed loop fuel trim actuals, and will also pull or add timing in different RPM/Load ranges based upon observed knock.
If you start having misfires or chronic knock, the ECU will try adjusting learning values first, and then pull back your IAM to a level that prevents detonation if it's bad.
If you have a tactrix cable, and run learning view on your vehicle, you can see all of these values.