diff --git a/cmd/update/update.go b/cmd/update/update.go
index e639a1de2..129ef4562 100644
--- a/cmd/update/update.go
+++ b/cmd/update/update.go
@@ -358,15 +358,6 @@ func validateSkillsLayoutOptions(opts *UpdateOptions) errs.TypedError {
 	if _, ok := skillscheck.NormalizeLayout(opts.SkillsLayout); !ok {
 		return errs.NewValidationError(errs.SubtypeInvalidArgument, "--skills-layout must be one of separate or hybrid").WithParam("--skills-layout")
 	}
-	layout, flat := resolveSkillsSyncOptions(opts.SkillsLayout, opts.FlatSkills, opts.FlatSet)
-	if layout != skillscheck.LayoutHybrid {
-		return nil
-	}
-	for _, skill := range flat {
-		if skill == "lark-shared" {
-			return errs.NewValidationError(errs.SubtypeInvalidArgument, "lark-shared cannot be selected by --flat-skills; it is managed automatically for lark-suite compatibility").WithParam("--flat-skills")
-		}
-	}
 	return nil
 }
 
diff --git a/cmd/update/update_test.go b/cmd/update/update_test.go
index 3a92dd0b1..9f2904b6f 100644
--- a/cmd/update/update_test.go
+++ b/cmd/update/update_test.go
@@ -1137,21 +1137,14 @@ func TestValidateSkillsLayoutOptionsRejectsSuiteMode(t *testing.T) {
 	}
 }
 
-func TestValidateSkillsLayoutOptionsRejectsSharedFlatInHybrid(t *testing.T) {
+func TestValidateSkillsLayoutOptionsAllowsFlatSkillsFilteringAfterOfficialDiscovery(t *testing.T) {
 	err := validateSkillsLayoutOptions(&UpdateOptions{
 		SkillsLayout: skillscheck.LayoutHybrid,
-		FlatSkills:   "lark-shared",
+		FlatSkills:   "lark-shared,lark-unknown",
 		FlatSet:      true,
 	})
-	if err == nil {
-		t.Fatal("validateSkillsLayoutOptions() err = nil, want validation error")
-	}
-	var validation *errs.ValidationError
-	if !errors.As(err, &validation) {
-		t.Fatalf("errors.As(err, *ValidationError) = false for %T", err)
-	}
-	if validation.Param != "--flat-skills" {
-		t.Fatalf("validation.Param = %q, want --flat-skills", validation.Param)
+	if err != nil {
+		t.Fatalf("validateSkillsLayoutOptions() err = %v, want nil", err)
 	}
 }
 
diff --git a/internal/skillscheck/layout.go b/internal/skillscheck/layout.go
index ae15a56f6..224d7c746 100644
--- a/internal/skillscheck/layout.go
+++ b/internal/skillscheck/layout.go
@@ -166,10 +166,10 @@ func resolveHybridSkillSets(layout string, requestedFlat, official []string, ski
 	effectiveFlat := map[string]bool{}
 	for _, skill := range uniqueSorted(requestedFlat) {
 		if skill == sharedSkillName {
-			return nil, nil, fmt.Errorf("%s cannot be selected by --flat-skills", sharedSkillName)
+			continue
 		}
 		if !officialSet[skill] {
-			return nil, nil, fmt.Errorf("flat skill %q is not in official skills", skill)
+			continue
 		}
 		configuredFlat[skill] = true
 		if !deletedSet[skill] {
diff --git a/internal/skillscheck/sync_test.go b/internal/skillscheck/sync_test.go
index d8a1a97da..8e6f06ae7 100644
--- a/internal/skillscheck/sync_test.go
+++ b/internal/skillscheck/sync_test.go
@@ -867,23 +867,39 @@ func TestSyncSkills_HybridWithNoFlatSkillsDoesNotKeepSharedTopLevel(t *testing.T
 	}
 }
 
-func TestSyncSkills_HybridRejectsSharedFlatSkill(t *testing.T) {
+func TestSyncSkills_HybridFiltersNonFlatOfficialSkills(t *testing.T) {
+	dir := t.TempDir()
+	t.Setenv("LARKSUITE_CLI_CONFIG_DIR", t.TempDir())
+
+	paths := map[string]string{}
+	for _, name := range []string{"lark-calendar", "lark-shared", "lark-suite"} {
+		paths[name] = filepath.Join(dir, name)
+		writeTestSkill(t, paths[name], name)
+	}
+
 	runner := &fakeSkillsRunner{
 		officialIndexOut: officialSkillsIndexOutput("lark-calendar", "lark-shared"),
-		globalJSONOut:    globalSkillsJSONOutput("lark-calendar", "lark-shared"),
+		globalJSONOut:    globalSkillsJSONFromPaths(paths),
 	}
 
 	result := SyncSkills(SyncOptions{
 		Version:    "1.0.33",
 		Layout:     LayoutHybrid,
-		FlatSkills: []string{"lark-shared"},
+		FlatSkills: []string{"lark-calendar", "lark-missing", "lark-shared"},
 		Runner:     runner,
 		Now:        time.Now,
 	})
 
-	if result.Err == nil || !strings.Contains(result.Err.Error(), "lark-shared") {
-		t.Fatalf("SyncSkills() err = %v, want lark-shared validation error", result.Err)
+	if result.Err != nil {
+		t.Fatalf("SyncSkills() err = %v, want nil", result.Err)
 	}
+	assertStrings(t, result.Flat, []string{"lark-calendar"})
+
+	state, readable, err := ReadState()
+	if err != nil || !readable {
+		t.Fatalf("ReadState() = (_, %v, %v), want readable", readable, err)
+	}
+	assertStrings(t, state.FlatSkills, []string{"lark-calendar"})
 }
 
 func TestSyncSkills_ParseEmptyWithNonEmptyStdoutFallsBack(t *testing.T) {