The part of the DVR functionality that was ruled to be in violation of Tivo's patent was the "watch one show while recording another" function, as several people had pointed out. But it's more complicated than that. Specifically, the patent describes a way of dynamically juggling two data streams in memory (the show being recorded and the show being watched) with only one processor and one hard drive. Tivo's patent describes this as a way to keep hardware costs down.
So, theoretically, if you built a DVR with two separate sets of processors, memory chips and hard drives, you could duplicate Tivo functionality without violating the patent. Perhaps there are other simpler ways to do this with one processor and one memory chip and still not violate the patent, but I have not studied the language in the patent so I don't know.
Now we really don't know what Dish's engineers could be cooking up. It's reasonable to assume that whatever they come up with will be a compromise of some sort (ie. the DVRs won't work as well or they will loose functionality). I'm hopefull that the 622 can be spared, because it's more powerful than the other DVRs, having three tuners and a CPU capable of juggling all that data at once. That leads me to believe the engineers have more flexibility. And, if I'm not mistaken, wasn't the Tivo lawsuit filed before the 622 came out? If so, perhaps Dish anticipated this and added some design features to address it, just in case.
In any event, I would look at the software modifications as a "stopgap measure" just in case. In otherwords, it's their last resort option if legal avenues dont' work. The engineers probably don't even know if they CAN create a workable software solution yet, but I'm sure they are trying. Hopefully it will never be needed though.