diff --git a/internal/datalifecycle/datalifecycle.go b/internal/datalifecycle/datalifecycle.go
index 85babc9a..12746f0a 100644
--- a/internal/datalifecycle/datalifecycle.go
+++ b/internal/datalifecycle/datalifecycle.go
@@ -588,15 +588,27 @@ func dirBytes(path string) (int64, error) {
 	return total, err
 }
 
+// removeEmptyParents removes empty layout directories above attempt dirs. It
+// never enters or removes an attempt dir: a live run creates artifact subdirs
+// (such as agent-logs/thread-analysis) before writing to them, so an empty
+// subdir there is still in use.
 func removeEmptyParents(root string) error {
 	var dirs []string
 	if err := filepath.WalkDir(root, func(path string, entry fs.DirEntry, err error) error {
 		if err != nil {
 			return err
 		}
-		if entry.IsDir() && path != root {
-			dirs = append(dirs, path)
+		if !entry.IsDir() || path == root {
+			return nil
+		}
+		isAttempt, err := isAttemptDir(root, path)
+		if err != nil {
+			return err
+		}
+		if isAttempt {
+			return filepath.SkipDir
 		}
+		dirs = append(dirs, path)
 		return nil
 	}); err != nil {
 		if errors.Is(err, fs.ErrNotExist) {
diff --git a/internal/datalifecycle/datalifecycle_test.go b/internal/datalifecycle/datalifecycle_test.go
index 347c1b4c..a1f4d8b3 100644
--- a/internal/datalifecycle/datalifecycle_test.go
+++ b/internal/datalifecycle/datalifecycle_test.go
@@ -483,3 +483,30 @@ func TestPruneKeepsOrphansWithinGraceWindow(t *testing.T) {
 		t.Fatalf("stale orphan stat error = %v, want not exist", err)
 	}
 }
+
+// Regression for #699: a live run's empty artifact subdirs must survive the
+// empty-dir sweep, while empty layout parents left by deleted runs go away.
+func TestPruneKeepsEmptyArtifactSubdirsOfLiveRuns(t *testing.T) {
+	layout := testLayout(t)
+	live := testRun(layout, "live", ledger.PostModeLive, testNow())
+	threadLogs := filepath.Join(live.ArtifactPath, "agent-logs", "thread-analysis")
+	if err := os.MkdirAll(threadLogs, 0o700); err != nil {
+		t.Fatalf("MkdirAll(thread logs): %v", err)
+	}
+	emptyParent := filepath.Join(layout.DataRoot, "runs", "github_owner_repo_2", "cccccccccccccccccccccccccccccccccccccccc")
+	if err := os.MkdirAll(emptyParent, 0o700); err != nil {
+		t.Fatalf("MkdirAll(empty parent): %v", err)
+	}
+	store := &fakeStore{runs: []ledger.Run{live}}
+	keep := 10
+
+	if _, err := Prune(context.Background(), Options{Layout: layout, Store: store, Now: testNow}, PruneOptions{KeepLast: &keep}); err != nil {
+		t.Fatalf("Prune: %v", err)
+	}
+	if _, err := os.Stat(threadLogs); err != nil {
+		t.Fatalf("live run's empty thread-analysis dir was removed: %v", err)
+	}
+	if _, err := os.Stat(filepath.Dir(emptyParent)); !errors.Is(err, os.ErrNotExist) {
+		t.Fatalf("empty layout parent stat error = %v, want not exist", err)
+	}
+}
diff --git a/internal/llm/subprocess.go b/internal/llm/subprocess.go
index e4cb0b2e..a5182a6d 100644
--- a/internal/llm/subprocess.go
+++ b/internal/llm/subprocess.go
@@ -5,6 +5,7 @@ import (
 	"io"
 	"os"
 	"os/exec"
+	"path/filepath"
 	"strings"
 	"sync"
 	"time"
@@ -290,6 +291,12 @@ func openSubprocessLog(path string) (*os.File, error) {
 	if strings.TrimSpace(path) == "" {
 		return nil, nil
 	}
+	// Create the parent at open time: callers create artifact dirs early, and an
+	// empty log dir can be pruned before a resumed task first writes to it.
+	// #nosec G301 G703 -- the parent is the caller-selected private artifact log directory.
+	if err := os.MkdirAll(filepath.Dir(path), 0o700); err != nil {
+		return nil, err
+	}
 	// #nosec G304 -- LogPath is an explicit caller-selected artifact path for tailable adapter logs.
 	return os.Create(path)
 }
diff --git a/internal/llmadapters/subprocess_test.go b/internal/llmadapters/subprocess_test.go
index 4a7b2c8b..8a5c27a9 100644
--- a/internal/llmadapters/subprocess_test.go
+++ b/internal/llmadapters/subprocess_test.go
@@ -912,6 +912,29 @@ func TestSubprocessCodexSafetyModes(t *testing.T) {
 		}
 	})
 
+	t.Run("resume creates a missing log directory", func(t *testing.T) {
+		// Regression for #699: a resumed thread analysis failed before launch
+		// when its agent-logs/thread-analysis directory no longer existed.
+		tempDir := t.TempDir()
+		recordPath := filepath.Join(tempDir, "records.jsonl")
+		logPath := filepath.Join(tempDir, "agent-logs", "thread-analysis", "thread-1.jsonl")
+		adapter := newCodexHelperAdapter("success", recordPath, 5*time.Second)
+		stream, err := adapter.Resume(context.Background(), "prior-session", Request{
+			Model:   "gpt-5.5",
+			Prompt:  "resume prompt",
+			LogPath: logPath,
+		})
+		if err != nil {
+			t.Fatalf("Resume: %v", err)
+		}
+		if _, err := stream.Wait(context.Background()); err != nil {
+			t.Fatalf("Wait: %v", err)
+		}
+		if _, err := os.Stat(logPath); err != nil {
+			t.Fatalf("Stat(log): %v", err)
+		}
+	})
+
 	for _, tt := range []struct {
 		name      string
 		sessionID string