Has the battery in the car been unplugged at all? Sometimes the red light indicates it needs 're-syncing', but I'm assuming you can open the car and drive normally anyway, which might mean that's a useless path to look at...
Is it possible the car key batteries just need replacing? Although again, I'm guessing being a mk8, the car is only 6 or so months old, so that seems a bit odd, especially with both keys flashing.
Have a look on Audi/Skoda/Seat forums too, the key fobs are basically identical and someone might have other ideas across the range.