diff --git a/src/Mod/Create/kc_format.py b/src/Mod/Create/kc_format.py
index 21e7bcaa45..f893ab490e 100644
--- a/src/Mod/Create/kc_format.py
+++ b/src/Mod/Create/kc_format.py
@@ -162,34 +162,28 @@ class _KcFormatObserver:
                     f"kc_format: pre_reinject hook failed: {exc}\n"
                 )
         try:
+            # Ensure silo/manifest.json exists in entries and update modified_at.
+            # All manifest mutations happen here so only one copy is written.
+            if "silo/manifest.json" in entries:
+                try:
+                    manifest = json.loads(entries["silo/manifest.json"])
+                except (json.JSONDecodeError, ValueError):
+                    manifest = _default_manifest()
+            else:
+                manifest = _default_manifest()
+            manifest["modified_at"] = datetime.now(timezone.utc).strftime(
+                "%Y-%m-%dT%H:%M:%SZ"
+            )
+            entries["silo/manifest.json"] = (
+                json.dumps(manifest, indent=2) + "\n"
+            ).encode("utf-8")
+
             with zipfile.ZipFile(filename, "a") as zf:
                 existing = set(zf.namelist())
-                # Re-inject cached silo/ entries
-                if entries:
-                    for name, data in entries.items():
-                        if name not in existing:
-                            zf.writestr(name, data)
-                            existing.add(name)
-                # Ensure silo/manifest.json exists
-                if "silo/manifest.json" not in existing:
-                    manifest = _default_manifest()
-                    zf.writestr(
-                        "silo/manifest.json",
-                        json.dumps(manifest, indent=2) + "\n",
-                    )
-                else:
-                    # Update modified_at timestamp
-                    raw = zf.read("silo/manifest.json")
-                    manifest = json.loads(raw)
-                    now = datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ")
-                    if manifest.get("modified_at") != now:
-                        manifest["modified_at"] = now
-                        # ZipFile append mode can't overwrite; write new entry
-                        # (last duplicate wins in most ZIP readers)
-                        zf.writestr(
-                            "silo/manifest.json",
-                            json.dumps(manifest, indent=2) + "\n",
-                        )
+                for name, data in entries.items():
+                    if name not in existing:
+                        zf.writestr(name, data)
+                        existing.add(name)
         except Exception as e:
             FreeCAD.Console.PrintWarning(
                 f"kc_format: failed to update .kc silo/ entries: {e}\n"
@@ -209,17 +203,36 @@ def update_manifest_fields(filename, updates):
         return
     if not os.path.isfile(filename):
         return
+    import shutil
+    import tempfile
+
     try:
-        with zipfile.ZipFile(filename, "a") as zf:
-            if "silo/manifest.json" not in zf.namelist():
-                return
-            raw = zf.read("silo/manifest.json")
-            manifest = json.loads(raw)
-            manifest.update(updates)
-            zf.writestr(
-                "silo/manifest.json",
-                json.dumps(manifest, indent=2) + "\n",
-            )
+        fd, tmp = tempfile.mkstemp(suffix=".kc", dir=os.path.dirname(filename))
+        os.close(fd)
+        try:
+            with (
+                zipfile.ZipFile(filename, "r") as zin,
+                zipfile.ZipFile(tmp, "w", compression=zipfile.ZIP_DEFLATED) as zout,
+            ):
+                found = False
+                for item in zin.infolist():
+                    if item.filename == "silo/manifest.json":
+                        if found:
+                            continue  # skip duplicate entries
+                        found = True
+                        raw = zin.read(item.filename)
+                        manifest = json.loads(raw)
+                        manifest.update(updates)
+                        zout.writestr(
+                            item.filename,
+                            json.dumps(manifest, indent=2) + "\n",
+                        )
+                    else:
+                        zout.writestr(item, zin.read(item.filename))
+            shutil.move(tmp, filename)
+        except BaseException:
+            os.unlink(tmp)
+            raise
     except Exception as e:
         FreeCAD.Console.PrintWarning(f"kc_format: failed to update manifest: {e}\n")