You're right he is thumping his legs as a warning, rabbits do that to warn others of danger. It's really hard for us humans to pin point what the cause can be sometimes, it can be a smell not just a noise. My rabbit thumped and hid when we cooked sausages once and the last time she thumped it was when I was running a bubble bath, she obviously wasn't impressed with my new purchase :lol: The first time she thumped we had absolutely no idea what it was? Gave us a fright though!
Some smells, however nice they smell to us, can scare them so maybe see if you can think of anything that you've changed recently, a washing powder, a new perfume or hand wash maybe? Is there a noise that only happens at night like a noisy boiler or pipes? If a window is open he may be able to smell a fox without actually seeing it. How long have you had the rabbit, have you had him for the 4 years?