As long as the alarm wasn't armed when you disconnected battery power, you don't have to do anything special like the configuration routine. I've disconnected and reconnected the battery many times and never had the issue you describe, and never had to reconfigure the alarm system after reconnecting the battery.
How fast and for how long does the light flash? If it flashes once every second, that's an indicator that the battery was disconnected and reconnected while the alarm was armed, or there was a failed attempt to enter the personal security code. A flash every two seconds indicates the system is armed, and a rapid flash of 3 times per second indicates the system is in personal code entry mode and is awaiting input.
If you think you may have disconnected the battery while the system was armed, try disarming the system and then disconnect the battery for a few minutes, then reconnect the battery.
Jerry