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You're probably missing the vxlan kernel module on the new kernel. It's not included in the default kernel package for Pi. This is covered in the k3s docs.

That sounds plausible. I saw it in the docs, but didn't consider it because I'm not using ubuntu, I'm using DietPi. Of course, I should have realised it could be relevant, because dietpi is based on debian, and it wouldn't surprise me if the vxlan in separate module comes from debian originally. I'll look into it, thanks!