diff --git a/README.md b/README.md
index 92cdc8ff59..ead9314a4b 100644
--- a/README.md
+++ b/README.md
@@ -2018,6 +2018,11 @@ the stable English `name`. API callers can pass `display_name` to agent creation
 or update requests; an omitted update preserves it and `null` clears it. The
 same optional field is supported in the agent's `config.yaml`.
 
+Custom Agents migrated to `agent_storage.backend: db` remain editable through
+Agent settings and `update_agent` while the importer retains their old files
+for rollback. See [Agent Storage](backend/docs/CONFIGURATION.md#agent-storage)
+for the migration procedure.
+
 Custom Agents can also be moved between DeerFlow users or deployments from the
 Agents gallery. **Export Agent** downloads a versioned
 `*.deerflow-agent.json` package containing the portable definition and
diff --git a/backend/app/gateway/routers/AGENTS.md b/backend/app/gateway/routers/AGENTS.md
index 9904a14366..cb3f9e6564 100644
--- a/backend/app/gateway/routers/AGENTS.md
+++ b/backend/app/gateway/routers/AGENTS.md
@@ -16,6 +16,11 @@ create-only: collisions return 409, never overwrite or upsert. Ordinary creation
 and import share `_persist_new_agent`, which uses `run_drained_write` so a
 cancelled request still drains the owned persistence worker.
 
+Custom Agent update guards apply legacy shared-file checks only when the
+resolved store is `FileAgentStore`, including the `update_agent` tool. DB
+imports retain source files for rollback; those files cannot veto SQL updates.
+Keep store resolution and filesystem checks off-loop in the HTTP route.
+
 Committed MCP reconciliation failures are logged once by
 `fail_mcp_reconciliation`, with only the underlying exception type.
 `_run_drained_mcp_apply` passes `_McpCommittedReconciliationError` as an expected
diff --git a/backend/app/gateway/routers/agents.py b/backend/app/gateway/routers/agents.py
index 459f520aa5..5415de97b9 100644
--- a/backend/app/gateway/routers/agents.py
+++ b/backend/app/gateway/routers/agents.py
@@ -26,6 +26,7 @@ from deerflow.config.app_config import get_app_config
 from deerflow.config.paths import get_paths
 from deerflow.knowledge_scope import KnowledgeScope, canonicalize_knowledge_scope
 from deerflow.persistence.agents import AgentDeleteOutcome, AgentExistsError, get_agent_store
+from deerflow.persistence.agents.file import FileAgentStore
 from deerflow.runtime.user_context import get_effective_user_id
 
 logger = logging.getLogger(__name__)
@@ -532,15 +533,18 @@ async def update_agent(name: str, body: AgentUpdateRequest, request: Request) ->
         raise HTTPException(status_code=404, detail=f"Agent '{name}' not found")
 
     def _is_legacy_only_layout() -> bool:
+        # The DB importer retains legacy source files for rollback. They say
+        # nothing about the ownership of the active SQL definition.
+        if not isinstance(get_agent_store(), FileAgentStore):
+            return False
         # Require config.yaml, not bare directory existence — a per-user agent
         # directory can exist containing only memory.json (written the first
         # time this user chats with a legacy shared agent, before this route
         # is ever called). Bare .exists() would miss that case and let this
         # fall through to a silent fork of a brand-new config.yaml/SOUL.md
         # into the memory-only directory instead of blocking (mirrors
-        # resolve_agent_dir's guard, see #3390). The db backend has no legacy
-        # shared layout, so this file-only guard is a no-op there. The .exists()
-        # probes are filesystem IO, so they run off the event loop.
+        # resolve_agent_dir's guard, see #3390). Store resolution and the
+        # filesystem probes both run off the event loop.
         paths = get_paths()
         agent_dir = paths.user_agent_dir(user_id, name)
         legacy_dir = paths.agent_dir(name)
diff --git a/backend/docs/CONFIGURATION.md b/backend/docs/CONFIGURATION.md
index aafba34b00..f1d9296e6a 100644
--- a/backend/docs/CONFIGURATION.md
+++ b/backend/docs/CONFIGURATION.md
@@ -684,6 +684,10 @@ uv run --no-sync --project backend python backend/scripts/migrate_agents_to_db.p
 
 The importer is idempotent (already-present agents are skipped) and leaves the source files untouched, so reverting `agent_storage.backend` to `file` is a clean rollback. Agent *memory* (`memory.json`) is unaffected by this switch.
 
+With `backend: db`, retained legacy files do not block HTTP or `update_agent`
+updates to the imported SQL definitions. With `backend: file`, shared legacy
+agents still require the user-isolation migration before they can be updated.
+
 ### Tools
 
 Configure specific tools available to the agent:
diff --git a/backend/packages/harness/deerflow/tools/builtins/update_agent_tool.py b/backend/packages/harness/deerflow/tools/builtins/update_agent_tool.py
index 3474f616bd..b9682468f4 100644
--- a/backend/packages/harness/deerflow/tools/builtins/update_agent_tool.py
+++ b/backend/packages/harness/deerflow/tools/builtins/update_agent_tool.py
@@ -38,6 +38,7 @@ from deerflow.config.agents_config import load_agent_config, preserve_non_manage
 from deerflow.config.app_config import get_app_config
 from deerflow.config.paths import get_paths
 from deerflow.persistence.agents import get_agent_store
+from deerflow.persistence.agents.file import FileAgentStore
 from deerflow.runtime.user_context import resolve_runtime_user_id
 from deerflow.tools.types import Runtime
 
@@ -158,19 +159,16 @@ def update_agent(
     if model is not None and get_app_config().get_model_config(model) is None:
         return _err(f"Unknown model '{model}'. Pass a model name that exists in config.yaml's models section.")
 
-    paths = get_paths()
-    agent_dir = paths.user_agent_dir(user_id, agent_name)
-    legacy_dir = paths.agent_dir(agent_name)
-    # Require config.yaml, not bare directory existence — a per-user agent
-    # directory can exist containing only memory.json (written the first
-    # time this user chats with a legacy shared agent, before update_agent
-    # is ever called). Bare .exists() would miss that case and let this
-    # fall through to load_agent_config, which correctly resolves through
-    # to the legacy shared config via resolve_agent_dir, silently forking
-    # a brand-new config.yaml/SOUL.md into the memory-only directory
-    # instead of blocking (mirrors resolve_agent_dir's guard, see #3390).
-    if not (agent_dir / "config.yaml").exists() and (legacy_dir / "config.yaml").exists():
-        return _err(f"Agent '{agent_name}' only exists in the legacy shared layout and is not scoped to a user. Run scripts/migrate_user_isolation.py to move legacy agents into the per-user layout before updating.")
+    # SQL definitions are already owner-scoped; the importer leaves their
+    # file-backed sources in place for rollback (#6743).
+    if isinstance(get_agent_store(), FileAgentStore):
+        paths = get_paths()
+        agent_dir = paths.user_agent_dir(user_id, agent_name)
+        legacy_dir = paths.agent_dir(agent_name)
+        # A memory-only user directory must not shadow the shared definition
+        # or allow a silent per-user fork (see #3390).
+        if not (agent_dir / "config.yaml").exists() and (legacy_dir / "config.yaml").exists():
+            return _err(f"Agent '{agent_name}' only exists in the legacy shared layout and is not scoped to a user. Run scripts/migrate_user_isolation.py to move legacy agents into the per-user layout before updating.")
 
     try:
         existing_cfg = load_agent_config(agent_name, user_id=user_id)
diff --git a/backend/tests/test_agent_storage_backend.py b/backend/tests/test_agent_storage_backend.py
index 206f8d11dc..14db9bcb13 100644
--- a/backend/tests/test_agent_storage_backend.py
+++ b/backend/tests/test_agent_storage_backend.py
@@ -7,11 +7,16 @@ from types import SimpleNamespace
 
 import pytest
 import yaml
+from fastapi import FastAPI
+from fastapi.testclient import TestClient
 from sqlalchemy import create_engine
 
+from app.gateway.auth_middleware import AuthMiddleware
 from app.gateway.deps import _validate_agent_storage
+from app.gateway.routers import agents as agents_router
 from deerflow.config.agent_storage_config import AgentStorageConfig
-from deerflow.config.app_config import reset_app_config
+from deerflow.config.agents_api_config import load_agents_api_config_from_dict
+from deerflow.config.app_config import AppConfig, reset_app_config, set_app_config
 from deerflow.config.database_config import DatabaseConfig
 from deerflow.config.extensions_config import reset_extensions_config
 from deerflow.persistence.agents import get_agent_store, make_agent_store
@@ -23,6 +28,7 @@ from deerflow.persistence.managed_subagents.base import ManagedSubagentDefinitio
 from deerflow.persistence.managed_subagents.file import FileManagedSubagentStore
 from deerflow.persistence.managed_subagents.model import ManagedSubagentRow
 from deerflow.persistence.managed_subagents.sql import SqlManagedSubagentStore
+from deerflow.tools.builtins.update_agent_tool import update_agent
 
 
 def _cfg(agent_backend: str, db_backend: str, sqlite_dir: str = "/tmp/agent-store-test") -> SimpleNamespace:
@@ -156,6 +162,78 @@ def test_importer_dry_run_writes_nothing(file_home, monkeypatch):
     assert SqlManagedSubagentStore(cfg.database.app_sync_sqlalchemy_url).list() == []
 
 
+@pytest.mark.parametrize("backend", ["file", "db"])
+@pytest.mark.parametrize("memory_only", [False, True], ids=["no-user-dir", "memory-only-user-dir"])
+@pytest.mark.parametrize("surface", ["http", "tool"])
+def test_legacy_source_only_blocks_file_backed_updates(tmp_path, monkeypatch, backend, memory_only, surface):
+    """Retained migration sources must not override the active SQL store (#6743)."""
+    monkeypatch.setenv("DEER_FLOW_HOME", str(tmp_path))
+    monkeypatch.setattr("deerflow.config.paths._paths", None)
+    monkeypatch.setenv("DEER_FLOW_AUTH_DISABLED", "1")
+    monkeypatch.setenv("DEER_FLOW_ENV", "test")
+    monkeypatch.setenv("ENVIRONMENT", "test")
+    legacy = tmp_path / "agents" / "reviewer"
+    legacy.mkdir(parents=True)
+    original_config = "name: reviewer\ndescription: original\n"
+    (legacy / "config.yaml").write_text(original_config, encoding="utf-8")
+    (legacy / "SOUL.md").write_text("Review carefully.", encoding="utf-8")
+    user_dir = tmp_path / "users" / "default" / "agents" / "reviewer"
+    if memory_only:
+        user_dir.mkdir(parents=True)
+        (user_dir / "memory.json").write_text("{}", encoding="utf-8")
+
+    cfg = AppConfig(
+        models=[],
+        sandbox={"use": "deerflow.sandbox.local:LocalSandboxProvider"},
+        database={"backend": "sqlite", "sqlite_dir": str(tmp_path / "db")},
+        agent_storage={"backend": backend},
+    )
+    set_app_config(cfg)
+    load_agents_api_config_from_dict({"enabled": True})
+    try:
+        if backend == "db":
+            # Real file discovery, import and SQL writes; only the unrelated
+            # schema bootstrap is replaced by the fixture's real SQLite DDL.
+            importer = _patch_importer(monkeypatch, cfg)
+            monkeypatch.setattr(sys, "argv", ["migrate_agents_to_db"])
+            assert importer.main() == 0
+        store = get_agent_store()
+        assert store.get("reviewer", user_id="default").description == "original"
+        if backend == "db":
+            store.create("reviewer", {"name": "reviewer", "description": "other owner"}, "Other soul", user_id="other-user")
+
+        if surface == "http":
+            app = FastAPI()
+            app.add_middleware(AuthMiddleware)
+            app.include_router(agents_router.router)
+            with TestClient(app) as client:
+                assert client.get("/api/agents/reviewer").status_code == 200
+                response = client.put("/api/agents/reviewer", json={"description": "updated"})
+            assert response.status_code == (200 if backend == "db" else 409), response.text
+            if backend == "file":
+                assert "legacy shared layout" in response.json()["detail"]
+        else:
+            runtime = SimpleNamespace(context={"agent_name": "reviewer", "user_id": "default"}, tool_call_id="update-1")
+            message = update_agent.func(runtime=runtime, description="updated").update["messages"][0]
+            assert message.status == ("success" if backend == "db" else "error"), message.content
+            if backend == "file":
+                assert "legacy shared layout" in message.content
+
+        assert store.get("reviewer", user_id="default").description == ("updated" if backend == "db" else "original")
+        assert store.get_soul("reviewer", user_id="default") == "Review carefully."
+        if backend == "db":
+            assert store.get("reviewer", user_id="other-user").description == "other owner"
+            assert store.get_soul("reviewer", user_id="other-user") == "Other soul"
+        assert (legacy / "config.yaml").read_text(encoding="utf-8") == original_config
+        assert (legacy / "SOUL.md").read_text(encoding="utf-8") == "Review carefully."
+        assert not (user_dir / "config.yaml").exists()
+        if memory_only:
+            assert (user_dir / "memory.json").read_text(encoding="utf-8") == "{}"
+    finally:
+        load_agents_api_config_from_dict({})
+        reset_app_config()
+
+
 def test_importer_runs_when_only_managed_subagents_exist(tmp_path, monkeypatch):
     monkeypatch.setenv("DEER_FLOW_HOME", str(tmp_path))
     from deerflow.config import paths as paths_module