I think his odds for reelection would have been maybe a bit better than 50/50. Other red state Senate Dems with strong personal brands (Tester, Heitkamp, Manchin, etc) managed to get through 2012 successfully, and Nelson running for reelection might've scared some of the bigger NE Republicans out of the race (though keep in mind that the "big names" that ended up running OTL were upset in the primary by a random state senator). On the other hand, Bob Kerrey's much-vaunted comeback flamed out pretty badly, and Nebraska is still one of the reddest states in the union. So there would be some headwinds in Nelson's way.
Assuming he gets reelected? Doubt it changes much. It's just one vote and there's a good-sized amount of other moderate/conservative Democrats in the caucus after 2012. Assuming nothing else changes and Trump/Generic Republican wins in 2016, I guess it's possible that Nelson votes against DeVos's confirmation for SecEd, which would be decisive. I'm not certain there were other votes close enough for one additional Dem to swing the other way, and on many votes (some economic policy, Gorsuch, most Cabinet noms) I'd imagine Nelson would vote with the White House. At best he makes passing the AHCA or the 2017 tax bill more difficult - which admittedly is a pretty big impact.