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A step whose minibatches yield ONLY execution-lapse notes produces no body patches (analysts return empty-edits carriers, dropped by _normalise_patches), so skip_no_patches / skip_no_rewrite would `continue` before the appendix flush and silently discard every note of the step. This hit exactly the feature's target regime (mature skill body, failures classified as lapses): in c1_searchqa_def_g55_sar, 10/40 steps skipped this way and lost 95 notes total. Extract the flush block into _flush_skill_aware_appendix() and call it on the normal update path (unchanged behavior) AND on both skip branches before `continue`, so notes persist and appendix_notes.json / step_rec counters are recorded for skipped steps too. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>