Hi there, to that point (and given I have the same question as the author): I purchased a theme from studiopress and heavily modified it. Now version 2.0 came out and I am affected exactly by the problem you mentioned: I can't upgrade!
I understand that the main upgrades are made to the framework itself which you shouldn't touch, however the child themes mostly need some tweaking, so it's a pity to lose any functionality that comes with an upgrade. Right now, I will use winmerge to compare the code line by line, fortunately it's a small theme.
Anyway, I think it should be made a little clearer that when you buy a theme, you shouldn't modify it heavily if you want to enjoy the "lifetime theme upgrades"...
Thanks for your consideration!