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Initially you would need a full diagnostic code read to establish a diagnostic path based on codes present.
This could be caused by any number of things. Changing the batteries in the key only really affects the central locking remote side of the key.
Does this fault exist with both keys or just one? If it is more with one key then I would suspect a key fault in all probability. If the fault occurs with both keys then you could be looking at a module issue, a battery fault or even a wiring fault.
The diagnosis for this is probably best carried out at a Skoda Dealer who have the access to all of the technical data required.