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delete_marker_definition removed the def but left the inherited global-* copies on every link: it called stop_marker(), which rejects inherited markers (409), and the ControllerError was swallowed as a warning. The orphaned copies were in-memory only (_persist_markers filters inherited markers) so a restart hid the symptom, but during a running session they were undeletable via either the per-link or project API. Add the same inherited=True bypass that update_marker already has, and pass it from the def-delete fan-out so the copies are removed for real.