I was worried about a SNN-BOS-SFO itin myself, and found that although flight 211 does continue on to SFO at 2:35 at some times of year, for the flights I have (in November), the 2:35 BOS-SFO segment is still flight 165. Thanks for the heads-up though; I'll keep an eye on the flight numbers.

Edited to add: Given that this is a paid ticket, I wonder how a BOS-SFO sticker upgrade will work if it becomes a direct flight? Sounds like a problem for the best minds in the "seating department".