I saved after it says 'a strong presence is warming the area' or something. Does my legendary disappear or can I still get it? I didn't encounter it or it zoom on the legend. So far I did this with Zapdos, Cobalion, and Thundurus.
The legendary won't disappear if you soft reset. As long as you save after it tells you there's 'a strong presence in the area,' you're safe to reset. This is also the only way to get the legendaries as shinies (unless you're freakishly lucky and run into a shiny legendary without resetting at all).