diff --git a/backend/apps/outputs/outputs.py b/backend/apps/outputs/outputs.py
index 0c3d3172..65aced57 100644
--- a/backend/apps/outputs/outputs.py
+++ b/backend/apps/outputs/outputs.py
@@ -346,33 +346,41 @@ async def seed_workspace(body: WorkspaceSeedRequest):
             "already_seeded": already_seeded,
         }
 
-    # Legacy flat path; unchanged.
+    # Legacy flat path. Seed only fills in MISSING files; it never overwrites
+    # what's already on disk. A reopen re-sends the inline output.files snapshot,
+    # which lags behind whatever the agent just wrote to the workspace; writing it
+    # back reverted every edited file (new files survived, edited ones snapped to
+    # the snapshot). Disk wins once an app exists.
     if body.files:
         for rel_path, content in body.files.items():
             full_path = os.path.normpath(os.path.join(folder, rel_path))
             if not full_path.startswith(os.path.normpath(folder)):
                 continue
+            if os.path.exists(full_path):
+                continue
             os.makedirs(os.path.dirname(full_path), exist_ok=True)
             with open(full_path, "w", encoding="utf-8") as f:
                 f.write(content)
     else:
         for rel_path, content in VIEW_TEMPLATE_FILES.items():
             full_path = os.path.join(folder, rel_path)
+            if os.path.exists(full_path):
+                continue
             with open(full_path, "w", encoding="utf-8") as f:
                 f.write(content)
 
-    # Seed the workspace's SKILL.md with the LIVE skill content so an
-    # agent that Reads SKILL.md sees the same text the Skills page shows.
-    # Snapshot at workspace creation; subsequent edits don't rewrite
-    # already-seeded workspaces (the system-prompt injection in
-    # agent_manager reads live, so the agent always has the latest
-    # rules regardless of this on-disk copy).
-    with open(os.path.join(folder, "SKILL.md"), "w", encoding="utf-8") as f:
-        f.write(load_app_builder_skill())
+    # SKILL.md is a creation-time snapshot; the live rules reach the agent via
+    # the system-prompt injection regardless, so never rewrite an existing one.
+    skill_path = os.path.join(folder, "SKILL.md")
+    if not os.path.exists(skill_path):
+        with open(skill_path, "w", encoding="utf-8") as f:
+            f.write(load_app_builder_skill())
 
     if body.meta:
-        with open(os.path.join(folder, "meta.json"), "w", encoding="utf-8") as f:
-            json.dump(body.meta, f, indent=2)
+        meta_path = os.path.join(folder, "meta.json")
+        if not os.path.exists(meta_path):
+            with open(meta_path, "w", encoding="utf-8") as f:
+                json.dump(body.meta, f, indent=2)
 
     return {"path": os.path.abspath(folder), "template_mode": "flat"}
 
diff --git a/backend/tests/test_seed_no_clobber.py b/backend/tests/test_seed_no_clobber.py
new file mode 100644
index 00000000..3b62946a
--- /dev/null
+++ b/backend/tests/test_seed_no_clobber.py
@@ -0,0 +1,77 @@
+"""Seed must CREATE, never overwrite. Reopening an app re-POSTs the inline
+output.files snapshot, which lags behind whatever the agent last wrote to the
+workspace on disk; seeding it back used to revert every edited file while the
+agent's new files survived (edits looked half-reverted on the next export).
+
+Path constants are module-level, so (like test_versions) we monkeypatch them
+into a temp tree. seed_workspace is async; we drive it with asyncio.run from a
+sync test so the suite's bare-async-skip doesn't quietly no-op these."""
+import asyncio
+import os
+
+import pytest
+
+from backend.apps.outputs import outputs as outputs_mod
+from backend.apps.outputs.models import WorkspaceSeedRequest
+
+
+@pytest.fixture
+def ws_root(tmp_path, monkeypatch):
+    root = tmp_path / "ws"
+    root.mkdir()
+    monkeypatch.setattr(outputs_mod, "WORKSPACE_DIR", str(root))
+    return root
+
+
+def _seed(**kw):
+    return asyncio.run(outputs_mod.seed_workspace(WorkspaceSeedRequest(**kw)))
+
+
+def _read(folder, rel):
+    with open(os.path.join(folder, rel), encoding="utf-8") as f:
+        return f.read()
+
+
+def test_reopen_seed_preserves_agent_edits(ws_root):
+    wsid = "ws-reopen"
+    folder = os.path.join(str(ws_root), wsid)
+    os.makedirs(os.path.join(folder, "frontend", "src"))
+    # v1 on disk, captured into the inline snapshot the editor later autosaves.
+    with open(os.path.join(folder, "frontend", "src", "App.tsx"), "w") as f:
+        f.write("<h1>v1</h1>")
+    snapshot = {"frontend/src/App.tsx": "<h1>v1</h1>"}
+
+    # Agent advances the workspace to v2 on disk: edits a file, adds a new one.
+    with open(os.path.join(folder, "frontend", "src", "App.tsx"), "w") as f:
+        f.write("<h1>v2 agent</h1>")
+    with open(os.path.join(folder, "frontend", "src", "New.tsx"), "w") as f:
+        f.write("// new v2 file")
+
+    # Reopen replays the stale snapshot through seed.
+    _seed(workspace_id=wsid, files=snapshot, meta={"name": "App"})
+
+    assert _read(folder, "frontend/src/App.tsx") == "<h1>v2 agent</h1>"  # not reverted
+    assert os.path.exists(os.path.join(folder, "frontend", "src", "New.tsx"))  # survived
+
+
+def test_fresh_seed_materializes_saved_files(ws_root):
+    wsid = "ws-fresh"
+    folder = os.path.join(str(ws_root), wsid)
+    _seed(workspace_id=wsid,
+          files={"index.html": "<html>saved</html>", "style.css": "body{}"},
+          meta={"name": "Flat"})
+    assert _read(folder, "index.html") == "<html>saved</html>"
+    assert _read(folder, "style.css") == "body{}"
+
+
+def test_seed_fills_only_missing_files(ws_root):
+    wsid = "ws-partial"
+    folder = os.path.join(str(ws_root), wsid)
+    os.makedirs(folder)
+    with open(os.path.join(folder, "keep.txt"), "w") as f:
+        f.write("on-disk wins")
+    # snapshot wants to change keep.txt AND add gone.txt; only the missing one lands.
+    _seed(workspace_id=wsid,
+          files={"keep.txt": "snapshot loses", "gone.txt": "recreated"})
+    assert _read(folder, "keep.txt") == "on-disk wins"
+    assert _read(folder, "gone.txt") == "recreated"