Could be a range of things. The fact that everything carried on as normal shows how resilient aircraft are to this sort of thing. Could be:

Lightning strike (noise but no real change to the motion).
Compressor stall/surge on the engine. They just do this occasionally and normally recover.
Clear Air Turbulence. This just comes up on you suddenly, rather than anything sustained, often with a momentary loss of aircraft attitude. And as that's what the skipper said, I'd believe him.

Don't worry, the crew are trained for it all. And if they don't, then the autopilot will handle it.