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State-change log lines were written inline (org-log-into-drawer nil), where a line landing between a heading and its DEADLINE/SCHEDULED line broke org's planning-line parser and dropped the entry from agenda views. org also logged no-op "State X from X" transitions that carry no information.
Set org-log-into-drawer to t so state changes land in :LOGBOOK: drawers, and add an around-advice on org-add-log-setup that skips identical from/to transitions. The suppression decision lives in a pure predicate so it's tested without driving org-todo. This removes the cause rather than stripping the lines after they appear.
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