Just keep observing him. A spook in the middle of the night is quite common with rabbits. They hear frequences we cant hear, they pick up on scents we have no chance of picking up on. There’s nothing supernatural or weird about it, it’s just how rabbits function.
Rabbits can however hurt themselves if/when they panick. They can hurt a limb or a claw etc. All you can do is to try to observe your bun to notice if there’s a limp or a wound etc, and if there is, treat it.
There’s no telling what it was that spooked him, because our human senses are not at all as acute as a rabbit’s are. The important thing now is that he’s calmed down, is eating and showing you affection. His reaction was appropriate, because he was perceiving a threat -that he’s calmed down now when his humans are around and the threat is gone is appropriate too.
I have had similar things happen with every youngish bun I’ve had. It’s scary for the human, but it doesnt mean there’s sth really wrong. I always do the treat test -offer a very yummy, rare, treat, like a sunflower seed or pumpkin seed. If the bun takes it, the likelihood that it’ll be just fine is high.