Key Pairing

Hi, 

This is an odd one, but presumably someone can offer advice or a suggestion. 

Got My Mk1 Octavia, which came with 2 keys, one with the logo worn off so the often used one, and a pristine spare. 

Driving home I tried unlocking with both, but only the worn one worked. Not too surprised by the pristine one having a dead battery. 

Car went in for work, I lazily asked them to put a new battery in the pristine key, and when I get it back, both keys flash, but only the pristine one will now remotely open the car!?!?

Does the key need to be paired to the car somehow, and can one key override the other? But cars will work in the ignition, so I know they are both correct for the car. 

I changed the battery in my Bora's key about 2 years ago and both keys continued to open the car, so presumably it is the same system as the fobs are seemingly identical, save for logo badge. 

Thoughts

Eric

PS Have also asked the garage, but wanted you guys view on this, also this might help someone else.