Hi, My name is*****'m happy to help you. During our conversation, I may be presenting you with different things to try, and ask you some Questions to get a better understand of the issue so I can answer your question properly. So stick with me to the end, and I am sure we should be able to get this issue resolved for you!
When you get the Key System warning, it is because the battery was so low that the key system operation did not fully complete. So now you have this warning. I have a few tricks we can try to clear this out. Hopefully one of them will work.
First lock and unlock the car with the mechanical key. Hold the Infiniti logo on the remote over the start button and start the car holding the fob over the start button and continue to hold it there for 10 seconds..
After you do that, turn the car off. Open and close the door. Then press the start button and start the car and see if the warning is still present.
If it is, the next thing I would like you to try is to disconnect the negative battery cable for 15 mins. This will do a hard reset on the car. You will need to reprogram the auto up feature for the windows, but that is easy. Lets just get the warning clear before I share that part with you.
Give those two steps a try and let me know how you make out.