My bad, Floyd, you are correct.
I think you were right the first time. Yes, 99.7 HD2 is the signal that 97.9 is duplicating, but so many more people can receive 97.9 than 99.7 HD2, that 97.9 has to be considered the primary signal. If it weren't, they wouldn't be saying 99X at 97.9. They would be saying just 99X.