I know of at least one game that stores the hi score data in both places. I found out by accident because I exited the game too quickly (?).
Here was the scenario:
1. Default Dig Dug has 5 scores each of them being 10,000.
2. Played until I reached about 15,000 and let the game end.
3. Exited out too quick (?).
Now according to the hi file the score should have been the 15,000, but every time I loaded the game, it didn't have it, but still maintained the original score.
So I started nosing around the nv file and noticed that it too had hi score data as well.
To fix my problem, I just deleted both files and played again.

pkurby1 is correct in that you can use the hiscore.dat file (if you have the latest one) to get a lot of information.
And what's this FE secret he speaks of?