Just a quick update.
I had called the reservation center and checked back on the times I upgraded and it turns out that all the previous sectors in the past were upgraded all the way through i.e. PER-HKG-CCU.
It was just that the upgrade cost was ridiculously high this time and the initial confusion/doubt that took place made me want to double check this. Looks like I learnt something new
Thank you for all your inputs.
Smooth