The licensing model is working like this: you purchase a global threshold.
Meaning that you previously purchased a Developer Edition up to 1M LOC, and then you upgraded to a Developer Edition up to 5M. Your global threshold is now 5M LOC.
If your need is to analyse 6M LOC, you should go to the 10M LOC threshold (and go back to your Sales rep to ask for the correct quote for this new threshold).