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The read-clone refresh reused the orchestrator's token-less best-effort fetch, but _clone_repo scrubs the token from the remote URL — so on a PRIVATE repo the refresh fetch failed silently and the clone stayed frozen at clone-time, never seeing commits merged afterwards. The panel then showed "auto-derived defaults" for a project whose .roboco/conventions.yml was already on the default branch. Replace the refresh with a token-authenticated fetch + hard-reset to the default branch (the token is injected transiently into the fetch argv, mirroring the clone; the read clone is orchestrator-side and never mounted into an agent container). A public repo with no token still refreshes unauthenticated.