Immobiliser Light Flashing

Afternoon Guys, 

I am wondering if you can help me or point me in the right direction. 

I am in the middle of doing a remote central locking on my polo 9n3. I have just had the flip key cut after 2 attempts and now it works on locks and ignition. My plan was to swap over the transponder from my spare and then code the new comfort module. 

I am fully aware that if I do not swap the transponder over I need to get my key coded for the immobiliser but upon tested it in the ignition today the car started fine and continued to run? The Immobiliser light was flashing but the car drove fine. 

Does anyone know why it was allowed to continue running? If it is not likely to cut out, I wont bother doing the transponder swap to avoid risk of messing it up. 

Thank you in advance for any help 🙂