Thanks to all who responded, even though it was to confirm the terminal diagnosis. I guess it serves me right for neglecting it for two years (in my defense, I was pregnant or nursing for much of that time!).
I wanted to update that I contacted SD this morning and they suggested I send the fly in to see if it was a covered warranty. When I explained the timing of my trip, they offered instead to give me a 45% discount off any new tent on their web site, and to help expedite it to me (I'm paying for the 2-day shipping, but they said they would monitor for the order and make sure it went out today). Couldn't much argue with that! I'm bummed about the fly failure but their customer service was great, and I wanted to make sure I noted that.
@Elliott Wolin -- I think I am going to try your suggestion for re-waterproofing the fly at some point, to resurrect the Hyperlight for car camping. It's a decent tent despite being over 4lbs, and positively palatial for a 2P.
I chose a Vapor Light 2, by the way, since I am illogically attached to having a freestanding tent, and that was the lightest one they had. (their site says 3lbs 4 oz. though I'm usually skeptical of those numbers). I'll replace the stakes and ditch all the sacks and should be close to that though. It looks "cozy" though at 25 sq. ft, but I am a shorter female, as is my hiking partner, so hopefully we'll fit ok without having to cuddle!
All in all-- the wallet is a little lighter now, but so's my pack, by over a pound, so I guess that's the bright side.