Thumping is not rare 🙂
I think you did great. Since rabbits are flight animals, they tend to hate being lifted up or even touched when they’re scared. It just stresses them out further. Imo its better to talk to them in a calm, normal voice and to offer a small treat.
Offering a treat is good because it’s not just soothing, it’s also a way for you to assess how scared the bun is. A terrified bun wont take the treat. A moderately upset bun will take the treat and the likelihood that devouring the treat makes the bun forget about the perceived danger is high.
From your description this does seem to have been a response to a perceived threat -a rabbit’s senses of hearing and smell are vastly superior to ours, so even when we cant hear anything, the bun very well could have. Thumping is however not always about fear. It can be about frustration or anger. It can be a normal part of the zoomies -i e when the (young) bun races around in what seems like a frenzy, doing quick turns and binkies.