diff --git a/codex-rs/config/src/key_aliases.rs b/codex-rs/config/src/key_aliases.rs
index c0f2dea391..f2967f87b6 100644
--- a/codex-rs/config/src/key_aliases.rs
+++ b/codex-rs/config/src/key_aliases.rs
@@ -1,3 +1,5 @@
+//! Normalize config aliases before merging layers and reporting origins.
+
 use toml::Value as TomlValue;
 use toml::map::Map as TomlMap;
 
@@ -21,7 +23,7 @@ const CONFIG_KEY_ALIASES: &[ConfigKeyAlias] = &[
     },
 ];
 
-pub(crate) fn normalize_key_aliases(path: &[String], table: &mut TomlMap<String, TomlValue>) {
+fn normalize_table_key_aliases(path: &[String], table: &mut TomlMap<String, TomlValue>) {
     for alias in CONFIG_KEY_ALIASES {
         if path
             .iter()
@@ -36,24 +38,61 @@ pub(crate) fn normalize_key_aliases(path: &[String], table: &mut TomlMap<String,
     }
 }
 
-pub(crate) fn normalized_with_key_aliases(value: &TomlValue, path: &[String]) -> TomlValue {
+pub(crate) fn normalize_key_aliases(value: &TomlValue) -> TomlValue {
+    normalize_key_aliases_at_path(value, &[])
+}
+
+fn normalize_key_aliases_at_path(value: &TomlValue, path: &[String]) -> TomlValue {
     match value {
         TomlValue::Table(table) => {
             let mut normalized = TomlMap::new();
             for (key, child) in table {
                 let mut child_path = path.to_vec();
                 child_path.push(key.clone());
-                normalized.insert(key.clone(), normalized_with_key_aliases(child, &child_path));
+                normalized.insert(
+                    key.clone(),
+                    normalize_key_aliases_at_path(child, &child_path),
+                );
             }
-            normalize_key_aliases(path, &mut normalized);
+            normalize_table_key_aliases(path, &mut normalized);
             TomlValue::Table(normalized)
         }
         TomlValue::Array(items) => TomlValue::Array(
             items
                 .iter()
-                .map(|item| normalized_with_key_aliases(item, path))
+                .map(|item| normalize_key_aliases_at_path(item, path))
                 .collect(),
         ),
         _ => value.clone(),
     }
 }
+
+/// Normalize only base tables reached by the overlay, leaving unrelated raw config intact.
+///
+/// Config-edit table Upserts start from the raw user layer, not the normalized effective config.
+/// They use a sparse overlay and persist only the edited subtree, but compute the returned
+/// version from the whole in-memory config. Normalizing unrelated base tables would make
+/// that version disagree with the file on disk.
+///
+/// For example, given `[memories] no_memories_if_mcp_or_web_search = false` and
+/// `[agents] max_depth = 1`, upserting `agents` with `{ "max_depth": 2 }` must leave
+/// the memories alias untouched. Renaming it only in memory would cause the next write
+/// using the returned version to fail with `ConfigVersionConflict`, despite no intervening edit.
+pub(crate) fn normalize_base_key_aliases(
+    base: &mut TomlValue,
+    overlay: &TomlValue,
+    path: &mut Vec<String>,
+) {
+    if let TomlValue::Table(base) = base
+        && let TomlValue::Table(overlay) = overlay
+    {
+        normalize_table_key_aliases(path, base);
+        for (key, value) in overlay {
+            if let Some(existing) = base.get_mut(key) {
+                path.push(key.clone());
+                normalize_base_key_aliases(existing, value, path);
+                path.pop();
+            }
+        }
+    }
+}
diff --git a/codex-rs/config/src/merge.rs b/codex-rs/config/src/merge.rs
index 0ad63aecc8..ef67c26f72 100644
--- a/codex-rs/config/src/merge.rs
+++ b/codex-rs/config/src/merge.rs
@@ -1,5 +1,5 @@
+use crate::key_aliases::normalize_base_key_aliases;
 use crate::key_aliases::normalize_key_aliases;
-use crate::key_aliases::normalized_with_key_aliases;
 use codex_network_proxy::normalize_host;
 use toml::Value as TomlValue;
 
@@ -55,7 +55,9 @@ impl ShellEnvironmentPolicyFilterRepresentation {
 
 /// Merge config `overlay` into `base`, giving `overlay` precedence.
 pub fn merge_toml_values(base: &mut TomlValue, overlay: &TomlValue) {
-    merge_toml_values_at_path(base, overlay.clone(), &mut Vec::new());
+    let overlay = normalize_key_aliases(overlay);
+    normalize_base_key_aliases(base, &overlay, &mut Vec::new());
+    merge_toml_values_at_path(base, overlay, &mut Vec::new());
 }
 
 pub fn is_structured_feature_path<S: AsRef<str>>(path: &[S]) -> bool {
@@ -94,8 +96,6 @@ fn merge_toml_values_at_path(base: &mut TomlValue, overlay: TomlValue, path: &mu
     if let TomlValue::Table(base_table) = &mut *base
         && let TomlValue::Table(mut overlay_table) = overlay
     {
-        normalize_key_aliases(path, base_table);
-        normalize_key_aliases(path, &mut overlay_table);
         if is_network_domains_path(path) {
             normalize_network_domain_keys(base_table);
             normalize_network_domain_keys(&mut overlay_table);
@@ -141,12 +141,12 @@ fn merge_toml_values_at_path(base: &mut TomlValue, overlay: TomlValue, path: &mu
             if let Some(existing) = base_table.get_mut(&key) {
                 merge_toml_values_at_path(existing, value, path);
             } else {
-                base_table.insert(key, normalized_with_key_aliases(&value, path));
+                base_table.insert(key, value);
             }
             path.pop();
         }
     } else {
-        *base = normalized_with_key_aliases(&overlay, path);
+        *base = overlay;
     }
 }
 
diff --git a/codex-rs/config/src/merge_tests.rs b/codex-rs/config/src/merge_tests.rs
index 1c16565c49..2c09762751 100644
--- a/codex-rs/config/src/merge_tests.rs
+++ b/codex-rs/config/src/merge_tests.rs
@@ -729,3 +729,20 @@ exclude = []
         assert_eq!(base, overlay);
     }
 }
+
+#[test]
+fn sparse_overlay_preserves_unvisited_base_aliases() {
+    let mut base = parse_toml(
+        "[memories]\nno_memories_if_mcp_or_web_search = false\n[agents]\nmax_threads = 2",
+    );
+    let overlay = parse_toml("[agents]\nmax_depth = 3");
+
+    merge_toml_values(&mut base, &overlay);
+
+    assert_eq!(
+        base,
+        parse_toml(
+            "[memories]\nno_memories_if_mcp_or_web_search = false\n[agents]\nmax_concurrent_threads_per_session = 2\nmax_depth = 3",
+        ),
+    );
+}
diff --git a/codex-rs/config/src/state.rs b/codex-rs/config/src/state.rs
index 35b9f783c5..ec271fd820 100644
--- a/codex-rs/config/src/state.rs
+++ b/codex-rs/config/src/state.rs
@@ -5,7 +5,7 @@ use crate::format_config_layer_source;
 
 use super::fingerprint::record_origins;
 use super::fingerprint::version_for_toml;
-use super::key_aliases::normalized_with_key_aliases;
+use super::key_aliases::normalize_key_aliases;
 use super::merge::merge_toml_values;
 use crate::CloudConfigBundleLoader;
 use crate::ConfigLayer;
@@ -506,7 +506,7 @@ impl ConfigLayerStack {
         let mut provider_paths = vec!["features.network_proxy.credentials.".to_string()];
 
         for layer in self.layers_low_to_high() {
-            let config = normalized_with_key_aliases(&layer.config, &[]);
+            let config = normalize_key_aliases(&layer.config);
             if let Some(profiles) = config.get("profiles").and_then(TomlValue::as_table) {
                 provider_paths.extend(
                     profiles