There are many documented instances of deer, particularly large/trophy bucks, that are seen unsuspecting in one picture, looking at the camera in the next and never seen by that camera again.
As I said, they make the "low glow" infrared for a reason. Even "regular" infrared can bother wise, old deer. Regular, bright camera flashes will definitely scare many of them.
Does it scare all deer? Nope. Most? Probably not. Which ones? I don't know. What I do know, is that I don't want to guess which deer I'll see again and which ones I won't. After all, the whole point is learning what deer are around, not which ones used to be until my camera scared them away.