diff --git a/internal/copystructure/copystructure.go b/internal/copystructure/copystructure.go
index aa5510298..c55897aaa 100644
--- a/internal/copystructure/copystructure.go
+++ b/internal/copystructure/copystructure.go
@@ -89,7 +89,15 @@ func copyValue(original reflect.Value) (any, error) {
 		}
 		copied := reflect.MakeSlice(original.Type(), original.Len(), original.Cap())
 		for i := 0; i < original.Len(); i++ {
-			val, err := copyValue(original.Index(i))
+			elem := original.Index(i)
+
+			// Handle nil values in slices (e.g., interface{} elements that are nil)
+			if elem.Kind() == reflect.Interface && elem.IsNil() {
+				copied.Index(i).Set(elem)
+				continue
+			}
+
+			val, err := copyValue(elem)
 			if err != nil {
 				return nil, err
 			}
diff --git a/internal/copystructure/copystructure_test.go b/internal/copystructure/copystructure_test.go
index d1708dc75..b21af6460 100644
--- a/internal/copystructure/copystructure_test.go
+++ b/internal/copystructure/copystructure_test.go
@@ -113,6 +113,21 @@ func TestCopy_Slice(t *testing.T) {
 		input[0]["key1"] = "modified"
 		assert.Equal(t, "value1", resultSlice[0]["key1"])
 	})
+
+	t.Run("slice with nil elements", func(t *testing.T) {
+		input := []any{
+			"value1",
+			nil,
+			"value2",
+		}
+		result, err := Copy(input)
+		require.NoError(t, err)
+
+		resultSlice, ok := result.([]any)
+		require.True(t, ok)
+		assert.Equal(t, input, resultSlice)
+		assert.Nil(t, resultSlice[1])
+	})
 }
 
 func TestCopy_Map(t *testing.T) {
diff --git a/pkg/chart/common/util/coalesce.go b/pkg/chart/common/util/coalesce.go
index 07794a04a..6c72b3d56 100644
--- a/pkg/chart/common/util/coalesce.go
+++ b/pkg/chart/common/util/coalesce.go
@@ -302,6 +302,15 @@ func coalesceTablesFullKey(printf printFn, dst, src map[string]interface{}, pref
 	if dst == nil {
 		return src
 	}
+	// Track original non-nil src keys before modifying src
+	// This lets us distinguish between user nullifying a chart default vs
+	// user setting nil for a key not in chart defaults.
+	srcOriginalNonNil := make(map[string]bool)
+	for key, val := range src {
+		if val != nil {
+			srcOriginalNonNil[key] = true
+		}
+	}
 	for key, val := range dst {
 		if val == nil {
 			src[key] = nil
@@ -311,9 +320,13 @@ func coalesceTablesFullKey(printf printFn, dst, src map[string]interface{}, pref
 	// values.
 	for key, val := range src {
 		fullkey := concatPrefix(prefix, key)
-		if dv, ok := dst[key]; ok && !merge && dv == nil {
+		if dv, ok := dst[key]; ok && !merge && dv == nil && srcOriginalNonNil[key] {
+			// When coalescing (not merging), if dst has nil and src has a non-nil
+			// value, the user is nullifying a chart default - remove the key.
+			// But if src also has nil (or key not in src), preserve the nil
 			delete(dst, key)
 		} else if !ok {
+			// key not in user values, preserve src value (including nil)
 			dst[key] = val
 		} else if istable(val) {
 			if istable(dv) {
diff --git a/pkg/chart/common/util/coalesce_test.go b/pkg/chart/common/util/coalesce_test.go
index 871bfa8da..4eaf4be2b 100644
--- a/pkg/chart/common/util/coalesce_test.go
+++ b/pkg/chart/common/util/coalesce_test.go
@@ -731,3 +731,37 @@ func TestConcatPrefix(t *testing.T) {
 	assert.Equal(t, "b", concatPrefix("", "b"))
 	assert.Equal(t, "a.b", concatPrefix("a", "b"))
 }
+
+// TestCoalesceValuesEmptyMapWithNils tests the full CoalesceValues scenario
+// from issue #31643 where chart has data: {} and user provides data: {foo: bar, baz: ~}
+func TestCoalesceValuesEmptyMapWithNils(t *testing.T) {
+	is := assert.New(t)
+
+	c := &chart.Chart{
+		Metadata: &chart.Metadata{Name: "test"},
+		Values: map[string]any{
+			"data": map[string]any{}, // empty map in chart defaults
+		},
+	}
+
+	vals := map[string]any{
+		"data": map[string]any{
+			"foo": "bar",
+			"baz": nil, // explicit nil from user
+		},
+	}
+
+	v, err := CoalesceValues(c, vals)
+	is.NoError(err)
+
+	data, ok := v["data"].(map[string]any)
+	is.True(ok, "data is not a map")
+
+	// "foo" should be preserved
+	is.Equal("bar", data["foo"])
+
+	// "baz" should be preserved with nil value since it wasn't in chart defaults
+	_, ok = data["baz"]
+	is.True(ok, "Expected data.baz key to be present but it was removed")
+	is.Nil(data["baz"], "Expected data.baz key to be nil but it is not")
+}
diff --git a/pkg/kube/resource.go b/pkg/kube/resource.go
index d88b171f0..d6d08d589 100644
--- a/pkg/kube/resource.go
+++ b/pkg/kube/resource.go
@@ -79,7 +79,14 @@ func (r ResourceList) Intersect(rs ResourceList) ResourceList {
 	return r.Filter(rs.Contains)
 }
 
-// isMatchingInfo returns true if infos match on Name and GroupVersionKind.
+// isMatchingInfo returns true if infos match on Name, Namespace, Group and Kind.
+//
+// IMPORTANT: Version is intentionally excluded from the comparison. Resources
+// served by the same CRD at different API versions (e.g. v2beta1 vs v2beta2)
+// share the same underlying storage in the Kubernetes API server. Comparing
+// the full GroupVersionKind causes Difference() to treat a version change as
+// a resource removal + addition, which makes Helm delete the resource it just
+// created during upgrades. See https://github.com/helm/helm/issues/31768
 func isMatchingInfo(a, b *resource.Info) bool {
-	return a.Name == b.Name && a.Namespace == b.Namespace && a.Mapping.GroupVersionKind == b.Mapping.GroupVersionKind
+	return a.Name == b.Name && a.Namespace == b.Namespace && a.Mapping.GroupVersionKind.GroupKind() == b.Mapping.GroupVersionKind.GroupKind()
 }
diff --git a/pkg/kube/resource_test.go b/pkg/kube/resource_test.go
index ccc613c1b..41215a878 100644
--- a/pkg/kube/resource_test.go
+++ b/pkg/kube/resource_test.go
@@ -72,8 +72,8 @@ func TestIsMatchingInfo(t *testing.T) {
 
 	gvkDiffVersion := schema.GroupVersionKind{Group: "group1", Version: "diff", Kind: "pod"}
 	resourceInfoDiffVersion := resource.Info{Name: "name1", Namespace: "namespace1", Mapping: &meta.RESTMapping{GroupVersionKind: gvkDiffVersion}}
-	if isMatchingInfo(&resourceInfo, &resourceInfoDiffVersion) {
-		t.Error("expected resources not equal")
+	if !isMatchingInfo(&resourceInfo, &resourceInfoDiffVersion) {
+		t.Error("expected resources with different versions but same group and kind to be equal")
 	}
 
 	gvkDiffKind := schema.GroupVersionKind{Group: "group1", Version: "version1", Kind: "deployment"}