diff --git a/backend/pkg/docker/client.go b/backend/pkg/docker/client.go
index 6a114561..af5604d4 100644
--- a/backend/pkg/docker/client.go
+++ b/backend/pkg/docker/client.go
@@ -600,7 +600,11 @@ func (dc *dockerClient) Cleanup(ctx context.Context) error {
 func (dc *dockerClient) IsContainerRunning(ctx context.Context, containerID string) (bool, error) {
 	inspection, err := dc.client.ContainerInspect(ctx, containerID)
 	if err != nil {
-		return false, fmt.Errorf("container inspection failed: %w", err)
+		if !client.IsErrNotFound(err) {
+			return false, fmt.Errorf("container inspection failed: %w", err)
+		}
+		// a removed container is missing, not an inspection failure
+		return false, nil
 	}
 
 	// Check both Running state and health status if available
diff --git a/backend/pkg/docker/client_test.go b/backend/pkg/docker/client_test.go
index f7ae3a23..62de6f6e 100644
--- a/backend/pkg/docker/client_test.go
+++ b/backend/pkg/docker/client_test.go
@@ -13,6 +13,7 @@ import (
 	"time"
 
 	"github.com/docker/docker/api/types/container"
+	"github.com/docker/docker/client"
 )
 
 func TestStatContainerEntries_AllSucceed(t *testing.T) {
@@ -260,3 +261,79 @@ func failNames(failures []statFailure) map[string]bool {
 	}
 	return m
 }
+
+const probeImage = "alpine:3.20"
+
+// newDaemonClient binds a client to the local daemon, skipping the test when
+// none is reachable.
+func newDaemonClient(t *testing.T) *dockerClient {
+	t.Helper()
+
+	cli, err := client.NewClientWithOpts(client.FromEnv)
+	if err != nil {
+		t.Skipf("docker daemon unavailable: %v", err)
+	}
+
+	ctx := context.Background()
+	cli.NegotiateAPIVersion(ctx)
+	if _, err := cli.Ping(ctx); err != nil {
+		t.Skipf("docker daemon unavailable: %v", err)
+	}
+
+	return &dockerClient{client: cli}
+}
+
+// A flow keeps the id of its primary container in the database. When that
+// container is removed behind pentagi's back the id has to read as not running,
+// otherwise the flow can never rebuild it.
+func TestIsContainerRunningRemovedContainer(t *testing.T) {
+	dc := newDaemonClient(t)
+	ctx := context.Background()
+
+	created, err := dc.client.ContainerCreate(ctx, &container.Config{
+		Image:      probeImage,
+		Entrypoint: []string{"tail", "-f", "/dev/null"},
+	}, nil, nil, nil, "")
+	if client.IsErrNotFound(err) {
+		t.Skipf("%s is not present locally", probeImage)
+	}
+	if err != nil {
+		t.Fatalf("create probe container: %v", err)
+	}
+	t.Cleanup(func() {
+		dc.client.ContainerRemove(context.Background(), created.ID, container.RemoveOptions{Force: true})
+	})
+
+	if err := dc.client.ContainerStart(ctx, created.ID, container.StartOptions{}); err != nil {
+		t.Fatalf("start probe container: %v", err)
+	}
+
+	running, err := dc.IsContainerRunning(ctx, created.ID)
+	if err != nil || !running {
+		t.Fatalf("got running=%v err=%v, want true and no error", running, err)
+	}
+
+	if err := dc.client.ContainerRemove(ctx, created.ID, container.RemoveOptions{Force: true}); err != nil {
+		t.Fatalf("remove probe container: %v", err)
+	}
+
+	running, err = dc.IsContainerRunning(ctx, created.ID)
+	if err != nil {
+		t.Fatalf("removed container: got error %v, want none", err)
+	}
+	if running {
+		t.Fatal("removed container reported as running")
+	}
+}
+
+func TestIsContainerRunningUnknownContainer(t *testing.T) {
+	dc := newDaemonClient(t)
+
+	running, err := dc.IsContainerRunning(context.Background(), "pentagi-container-that-does-not-exist")
+	if err != nil {
+		t.Fatalf("unknown container: got error %v, want none", err)
+	}
+	if running {
+		t.Fatal("unknown container reported as running")
+	}
+}
diff --git a/backend/pkg/tools/tools.go b/backend/pkg/tools/tools.go
index a460e15d..c3d8b107 100644
--- a/backend/pkg/tools/tools.go
+++ b/backend/pkg/tools/tools.go
@@ -481,18 +481,24 @@ func (fte *flowToolsExecutor) SetGraphitiClient(client *graphiti.Client) {
 
 func (fte *flowToolsExecutor) Prepare(ctx context.Context) error {
 	if cnt, err := fte.db.GetFlowPrimaryContainer(ctx, fte.flowID); err == nil {
-		switch cnt.Status {
-		case database.ContainerStatusRunning:
-			fte.primaryID = cnt.ID
-			fte.primaryLID = cnt.LocalID.String
-			if err := fte.syncMissingFiles(ctx); err != nil {
-				containerName := PrimaryTerminalName(fte.cfg.TenantPrefix(), fte.flowID)
-				return fmt.Errorf("failed to sync missing files to container '%s': %w", containerName, err)
+		// the stored status goes stale when the container is removed outside pentagi
+		if cnt.Status == database.ContainerStatusRunning {
+			containerName := PrimaryTerminalName(fte.cfg.TenantPrefix(), fte.flowID)
+			running, err := fte.docker.IsContainerRunning(ctx, cnt.LocalID.String)
+			if err != nil {
+				return fmt.Errorf("failed to inspect container '%s': %w", containerName, err)
+			}
+			if running {
+				fte.primaryID = cnt.ID
+				fte.primaryLID = cnt.LocalID.String
+				if err := fte.syncMissingFiles(ctx); err != nil {
+					return fmt.Errorf("failed to sync missing files to container '%s': %w", containerName, err)
+				}
+				return nil
 			}
-			return nil
-		default:
-			fte.docker.RemoveContainer(ctx, cnt.LocalID.String, cnt.ID)
 		}
+
+		fte.docker.RemoveContainer(ctx, cnt.LocalID.String, cnt.ID)
 	}
 
 	// Explicit capability allow-list (CapDrop: ALL below): Docker's default 14