Andy was not stationary for 39 seconds. Much like the Cadel puncture on Sierra Nevada, it's been exaggerated in the re-telling because the chase from behind is more dramatic than the surge from in front (Cadel lost the Vuelta by more than he lost on that stage anyway so it's a moot point, but that didn't stop it being brought up time and again as the cause of the defeat). Andy lost 22 seconds on the descent because he's a rubbish descender. Andy wouldn't have been in that position if Fabian Cancellara wasn't a huge great whopping hypocrite anyway, because Cancellara would have neutralised stage 3 as well, and Contador would have been 1'13 further up than he already was. If crashes and accidents are just racing incidents, Andy loses time to Contador in stage 2 (how much, we don't know, as the Contador group was a minute or two behind when the neutralisation occurred, and the Schleck group over 4 minutes, but I don't recall who was in which group in terms of engines. Menchov was in the front group though, as miraculously he of all people had stayed upright when everybody else was falling over!!!). If they aren't, Contador should have the time he lost on stage 3 back. Saxo picked and chose which incidents were fair game and which weren't that year. Even if you argue that the crash of Martin and Fränk wasn't a justification, they didn't wait when Chavanel - in the maillot jaune - punctured. Hypocritical to then expect Contador to wait when you slip your chain two weeks later, huh? Even if Chavanel wasn't likely to be GC relevant after three weeks, there's more than enough intrigue to have hours of debate from the 2010 Tour. It was its only hope to compete with the 2010 Giro.
It's also impossible to extrapolate what would have happened as, had the chain incident not occurred, they wouldn't have had their little bromance on the Tourmalet and they might have attacked each other. I don't recall who was strongest that day or if we ever got to find out since they were joined at the hip.