Please charge your battery with a charger before you fry your charging system. It may need to be replaced. It may be too late for your charging system. When you drain the battery dead, there is still chemical energy left in the cells. If power draw is stopped, the battery will seem to charge itself and work again. In doing so, a part of the capacity is sacrificed forever. If the battery is drained empty more than a couple of times, it's time for a new battery.
To the car, a dead battery is an overload. Some vehicles are designed not to try to fully charge a dead battery. Most vehicles will burn the charging system up trying to do so. Same idea, if this happens much you will need a new alternator and maybe more parts.
I would definitely have the car serviced by a pro shop, with veteran mechanics. Discuss your concerns with the ignition and charging systems, and tell the tech about your power loss event. Symptoms such as this are better fixed before murphy's law kicks in and you are left stranded on the road somewhere. The repairs cost less before everything is destroyed as well.
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