I've seen people say that the odds are about 75 percent chance of getting the rune or upgrade back. However, from personal experience, I would have to say a little less than that. Something like 66 percent or 2/3rds of the time you will get the item back.
Odds are pretty good: I've been lucky enough to salvage back each and every rune or upgrade I've applied (about six or seven total) with none destroyed so far. The only hiccup is when I had two upgrades on a sword and only got one back.
Personally I have only lost one rune out of 10 when it comes to salvaging my armor. When it comes to salvaging weapon upgrades I drop to a 50/50 chance of getting the upgrade if there is only one of them on there. When there is 2 upgrades I drop to 1 in 3 of getting anything.