diff --git a/server/src/agents/pool/auto_assign/scan.rs b/server/src/agents/pool/auto_assign/scan.rs
index efd414c4..6f9be845 100644
--- a/server/src/agents/pool/auto_assign/scan.rs
+++ b/server/src/agents/pool/auto_assign/scan.rs
@@ -30,6 +30,9 @@ pub(super) fn scan_stage_items(project_root: &Path, stage_dir: &str) -> Vec<Stri
     }
 
     // Also include filesystem items (backwards compat / migration fallback).
+    // Skip any story the CRDT already tracks — its authoritative stage wins.
+    // Stale .md files in pipeline dirs (e.g. 1_backlog/) must not shadow an
+    // archived or otherwise-moved story in the CRDT.
     let dir = project_root.join(".huskies").join("work").join(stage_dir);
     if dir.is_dir()
         && let Ok(entries) = std::fs::read_dir(&dir)
@@ -39,6 +42,14 @@ pub(super) fn scan_stage_items(project_root: &Path, stage_dir: &str) -> Vec<Stri
             if path.extension().and_then(|e| e.to_str()) == Some("md")
                 && let Some(stem) = path.file_stem().and_then(|s| s.to_str())
             {
+                // If the CRDT knows about this story (any stage), trust the CRDT.
+                if crate::pipeline_state::read_typed(stem)
+                    .ok()
+                    .flatten()
+                    .is_some()
+                {
+                    continue;
+                }
                 items.insert(stem.to_string());
             }
         }
@@ -167,6 +178,39 @@ mod tests {
         }
     }
 
+    // ── Bug 556: stale filesystem shadow must not override CRDT stage ──────────
+    //
+    // A story file left in 1_backlog/ on disk but tracked as 6_archived in the
+    // CRDT must NOT appear when scanning 1_backlog.  Without the fix, the
+    // filesystem fallback would add it, causing promote_ready_backlog_stories to
+    // attempt to promote an archived story.
+    #[test]
+    fn scan_stage_items_skips_filesystem_item_known_to_crdt_at_different_stage() {
+        crate::db::ensure_content_store();
+        // Write the story into the CRDT as 6_archived.
+        crate::db::write_item_with_content(
+            "9970_story_archived",
+            "6_archived",
+            "---\nname: Archived\n---\n",
+        );
+
+        // Also place a stale .md file in a temp 1_backlog/ dir.
+        let tmp = tempfile::tempdir().unwrap();
+        let backlog = tmp.path().join(".huskies/work/1_backlog");
+        std::fs::create_dir_all(&backlog).unwrap();
+        std::fs::write(
+            backlog.join("9970_story_archived.md"),
+            "---\nname: Archived\n---\n",
+        )
+        .unwrap();
+
+        let items = scan_stage_items(tmp.path(), "1_backlog");
+        assert!(
+            !items.contains(&"9970_story_archived".to_string()),
+            "archived CRDT story must not appear in 1_backlog scan via stale filesystem shadow"
+        );
+    }
+
     #[test]
     fn scan_stage_items_returns_empty_for_missing_dir() {
         // Use a unique stage name that no other test writes to, so
diff --git a/server/src/chat/commands/coverage.rs b/server/src/chat/commands/coverage.rs
index ab36079a..b111704a 100644
--- a/server/src/chat/commands/coverage.rs
+++ b/server/src/chat/commands/coverage.rs
@@ -67,7 +67,9 @@ fn read_coverage_report(path: &std::path::Path) -> String {
     let report: CoverageReport = match serde_json::from_str(&content) {
         Ok(r) => r,
         Err(e) => {
-            return format!("**Coverage (cached)**\n\nFailed to parse `.coverage_report.json`: {e}");
+            return format!(
+                "**Coverage (cached)**\n\nFailed to parse `.coverage_report.json`: {e}"
+            );
         }
     };