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The vehicle has obviously not registered that there is a key inside the vehicle. This could be due to a fault with that key fob.
Even though the Spare Key Remote Fob doesn't work you should still be able to open the vehicle with the Spare Key Blade using the lock which is usually on the Passenger Side Front Door (although sometimes on the driver door) often behind a plastic cover which needs to be prised off. Once you have gained access to the vehicle it would need a full diagnostic code read to determine what code(s) are present. From there a diagnostic path can be established. The fault could lie in the following places:
Should the fault lie with the Key Fobs then replacements will be required and these will need to be coded at a Skoda Dealer.
In the same place as a conventional keyhole. Should be just to the rear of the handle but will probably be covered by a plastic cap which you have to lever off.
You have to remove the plastic cover to the rear of the door handle. The lock is underneath it!
Look at the following Website: Door Lock Access It shows an Octavia but they are in effect the same operation to gain access.
That's good. Glad you have it sorted.