I view the notice as a new lifetime program is coming out and the current programs (FLY ON and JGC) will stay as they are.

One important point is the lifetime program only counts mileage history and everything else such as spending with JAL card do not (only kicks in when the program goes live), so there is no immediate reason to kill JGC or drastically change FLY ON program. I do foresee JAL closing the JGC infinite Sapphire loop by either making it harder to qualify (which is already -ing mode by killing the domestic bonus and etc) or raise the required miles to maybe 10K or even 20K if required activities not met.