I had the same issue, luckily I was at home when it wouldn’t open. No warning I just got up and couldn’t open the car. So I got the spare only to find that wouldn’t open either.
I’ve had this in the past and found if I open the boot this allowed the car to then unlock fully by the key. Not this time, I didn’t think that both would have drained with in the same time scale. So remembered the key should unlock the door manually. Even that didn’t work so tried my phone which strangely did lock and unlock. The trouble is you cant rely on the app as the 12v battery warning comes on regularly, saying unable to wake car.
Got on the phone to the dealership who seemed perplexed at the situation and advise I call Skoda Direct for assistance. They called later that day and said the batteries are done. Changed them FOC, I said the spare is kept in my wife’s handbag and she never uses it. It only activates when she’s at the car before me, for the KESSY entrance. Where as I leave the house many more times than she.
I keep my key in a Farady pouch, which I was told about after the batteries running out within the first 4 months of ownership. I’m currently due to replace in Jan 27. It seems after the latest update the batteries are running out even quicker according to Skoda call out guy. He said the advice had changed regarding Faraday pouches too.
I felt like a really dope not checking the batteries before arranging a call out.