A Flux-managed Deployment is deleted with kubectl. What happens?

Why this is the answer

Flux runs controllers inside the cluster that continuously compare the cluster with the manifests in Git and re-apply what differs, so an out-of-band deletion is undone on the next interval — that convergence is the whole point of GitOps. Nothing needs re-bootstrapping, Flux never writes changes back as a proposal, and reconciliation is on by default rather than an extra feature.