diff --git a/internal/clientinject/engine.go b/internal/clientinject/engine.go
index d845984..a09f33c 100644
--- a/internal/clientinject/engine.go
+++ b/internal/clientinject/engine.go
@@ -129,6 +129,35 @@ func fileSHA1(w FileWriter, path string) (string, error) {
 	return hex.EncodeToString(sum[:]), nil
 }
 
+// stockPESHA1 returns the stock primary-PE SHA-1 for forensics / manifest PESHA1.
+//
+// Order:
+//  1. profile PrimaryBinary.SHA1 (authoritative stock fingerprint)
+//  2. sibling .openfsd-bak SHA-1 (post-Apply; live PE is patched)
+//  3. live PE SHA-1 (first-time / no bak — expected to equal stock)
+//
+// Never prefer a patched live hash when profile stock or bak is available.
+func stockPESHA1(w FileWriter, pe string, profile *Profile) string {
+	if profile != nil {
+		if s := strings.ToLower(strings.TrimSpace(profile.PrimaryBinary.SHA1)); s != "" {
+			return s
+		}
+	}
+	if pe == "" {
+		return ""
+	}
+	if w == nil {
+		w = OSFileWriter{}
+	}
+	if sum, err := fileSHA1(w, BackupPath(pe)); err == nil && sum != "" {
+		return sum
+	}
+	if sum, err := fileSHA1(w, pe); err == nil {
+		return sum
+	}
+	return ""
+}
+
 // normalizeInstall makes PrimaryPE absolute under RootDir when relative.
 func normalizeInstall(install Install) Install {
 	if pe := AbsPrimaryPE(install); pe != "" {
@@ -153,8 +182,10 @@ func (e *Engine) Plan(ctx context.Context, install Install, ep Endpoints) (*Plan
 	if install.ProfileID == "" {
 		install.ProfileID = profile.ProfileID
 	}
-	if install.HashSHA1 == "" && install.PrimaryPE != "" {
-		if sum, err := fileSHA1(e.writer(), install.PrimaryPE); err == nil {
+	// HashSHA1 / manifest PESHA1 must be the stock PE fingerprint, not a
+	// post-patch live digest (re-Plan after Apply leaves bak + patched PE).
+	if install.HashSHA1 == "" {
+		if sum := stockPESHA1(e.writer(), install.PrimaryPE, profile); sum != "" {
 			install.HashSHA1 = sum
 		}
 	}
@@ -214,6 +245,8 @@ func (e *Engine) Apply(ctx context.Context, plan *Plan) (*ApplyResult, error) {
 	// On first apply (no stock bak for PE yet), PE must match profile stock SHA.
 	// Re-apply after a prior successful inject keeps stock in .openfsd-bak while
 	// the live PE may already be patched — skip live-hash stock check then.
+	// HashSHA1 / manifest PESHA1 always record stock identity (profile or bak),
+	// never a patched live digest.
 	if plan.Install.PrimaryPE != "" {
 		want := strings.ToLower(strings.TrimSpace(profile.PrimaryBinary.SHA1))
 		bak := BackupPath(plan.Install.PrimaryPE)
@@ -226,11 +259,9 @@ func (e *Engine) Apply(ctx context.Context, plan *Plan) (*ApplyResult, error) {
 				return nil, fmt.Errorf("clientinject: PE sha1 %s does not match profile %s stock %s",
 					sum, profile.ProfileID, want)
 			}
-			plan.Install.HashSHA1 = sum
-		} else if plan.Install.HashSHA1 == "" {
-			if sum, err := fileSHA1(w, plan.Install.PrimaryPE); err == nil {
-				plan.Install.HashSHA1 = sum
-			}
+		}
+		if stock := stockPESHA1(w, plan.Install.PrimaryPE, profile); stock != "" {
+			plan.Install.HashSHA1 = stock
 		}
 	}
 	if err := a.Verify(plan.Install, profile); err != nil {
diff --git a/internal/clientinject/engine_test.go b/internal/clientinject/engine_test.go
index 83ebd8f..0167a62 100644
--- a/internal/clientinject/engine_test.go
+++ b/internal/clientinject/engine_test.go
@@ -9,6 +9,7 @@ import (
 	"fmt"
 	"os"
 	"path/filepath"
+	"strings"
 	"testing"
 )
 
@@ -767,6 +768,78 @@ func TestEngine_PlanFillsHash(t *testing.T) {
 	}
 }
 
+// After Apply the live PE may be patched; re-Plan with empty HashSHA1 must still
+// record stock (profile/bak) for HashSHA1, and re-Apply manifest PESHA1 must match stock.
+func TestEngine_RePlanHashSHA1IsStockNotLive(t *testing.T) {
+	root := t.TempDir()
+	pe := filepath.Join(root, "app.exe")
+	payload := filepath.Join(root, "payload.bin")
+	stockPE := []byte("MZ-fake-pe")
+	patchedPE := []byte("MZ-PATCHED-PE-CONTENT")
+	if err := os.WriteFile(pe, stockPE, 0o644); err != nil {
+		t.Fatal(err)
+	}
+	if err := os.WriteFile(payload, []byte("STOCK-PAYLOAD"), 0o644); err != nil {
+		t.Fatal(err)
+	}
+	stockSum := sha1hex(stockPE)
+	store := NewProfileStore()
+	_ = store.Add(&Profile{
+		SchemaVersion: 2, ProfileID: "fake-1", ClientID: "fake",
+		PrimaryBinary: PrimaryBinarySpec{RelativePath: "app.exe", SHA1: stockSum},
+	})
+	fake := &FakeAdapter{ID: "fake", NewData: []byte("OPENFSD-PATCHED")}
+	eng := NewEngine(store, fake)
+	install := Install{
+		ClientID: "fake", RootDir: root, PrimaryPE: pe, ProfileID: "fake-1",
+	}
+	plan, err := eng.Plan(context.Background(), install, Endpoints{WebBaseURL: "https://a/"})
+	if err != nil {
+		t.Fatal(err)
+	}
+	if _, err := eng.Apply(context.Background(), plan); err != nil {
+		t.Fatal(err)
+	}
+	// Simulate PE body mutation (real adapters patch the PE; FakeAdapter only
+	// rewrites payload.bin — write a patched PE while bak holds stock).
+	if err := os.WriteFile(pe, patchedPE, 0o644); err != nil {
+		t.Fatal(err)
+	}
+	// Bak must still be stock from first Apply.
+	bak, err := os.ReadFile(pe + BackupSuffix)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if !bytes.Equal(bak, stockPE) {
+		t.Fatalf("bak=%q", bak)
+	}
+
+	// Re-Plan without HashSHA1 / with only RootDir+PE — must fill stock, not live.
+	plan2, err := eng.Plan(context.Background(), Install{
+		ClientID: "fake", RootDir: root, PrimaryPE: pe, ProfileID: "fake-1",
+	}, Endpoints{WebBaseURL: "https://a/"})
+	if err != nil {
+		t.Fatal(err)
+	}
+	if plan2.Install.HashSHA1 != stockSum {
+		t.Fatalf("re-plan HashSHA1=%q want stock %q (not live %q)",
+			plan2.Install.HashSHA1, stockSum, sha1hex(patchedPE))
+	}
+
+	// Re-Apply: manifest PESHA1 must be stock.
+	plan2.Mutations = plan.Mutations // reuse write mutation
+	if _, err := eng.Apply(context.Background(), plan2); err != nil {
+		t.Fatal(err)
+	}
+	m, err := ReadManifest(OSFileWriter{}, root)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if !strings.EqualFold(m.PESHA1, stockSum) {
+		t.Fatalf("manifest PESHA1=%q want stock %q", m.PESHA1, stockSum)
+	}
+}
+
 func TestNewEngine_NilAdapterSkipped(t *testing.T) {
 	eng := NewEngine(NewProfileStore(), nil, &FakeAdapter{ID: "x"})
 	if eng.Adapters["x"] == nil {
diff --git a/internal/clientinject/vpilotconfig/vpilotconfig.go b/internal/clientinject/vpilotconfig/vpilotconfig.go
index 5b691d5..a11fe8a 100644
--- a/internal/clientinject/vpilotconfig/vpilotconfig.go
+++ b/internal/clientinject/vpilotconfig/vpilotconfig.go
@@ -14,6 +14,20 @@
 // Prefer Rewrite (or ParseDocument + Document.Format) when updating an existing
 // install config: unknown elements and attributes are preserved. Format alone
 // emits a minimal four-field document and is for synthetic fixtures only.
+//
+// # encoding/xml fidelity limits
+//
+// Round-trip uses encoding/xml with a generic element tree (xml:",any"). That
+// preserves unknown elements and their attributes for normal vPilot configs,
+// but does **not** preserve:
+//   - XML comments (<!-- ... -->)
+//   - processing instructions
+//   - exact original whitespace, indentation, or attribute order
+//   - document type declarations / entity expansions beyond the stdlib decoder
+//
+// Acceptable for Phase 0 (vPilot writes machine-generated field values). Operators
+// who hand-edit vPilotConfig.xml with comments should expect comments to be
+// dropped on Apply; re-add comments after inject if needed.
 package vpilotconfig
 
 import (