How does the audit run's stage move — Planning, Fieldwork, Queries, Filing, Closed?

The stage is derived from facts, never a tick: packs issued, the auditor's questions open or answered, and each company's signed accounts and CT600 recorded as filed (Final with the date it went in, or Companies House's record — a draft never counts). You can set a different stage only as an override with a reason, and Follow the facts clears it. A run closes when the checklist on Filings & close is clear; a closed run can be reopened and the reopening is recorded.