upsert_reference only wrote loader_path on the INSERT branch, so
re-ingesting an existing reference (an output overwritten in place, or a
file re-registered after its loader_path derivation changed) kept the
stale or NULL value forever. Write it on the UPDATE branch too, with a
null-safe change guard so a loader_path difference alone is enough to
trigger the update, and identical values stay a no-op.
