diff --git a/deps/deps.go b/deps/deps.go
index e5dc339a4..da0db6e9d 100644
--- a/deps/deps.go
+++ b/deps/deps.go
@@ -2,6 +2,7 @@
 package deps
 
 import (
+	"bytes"
 	"context"
 	"crypto/rand"
 	"database/sql"
@@ -429,6 +430,11 @@ func LoadConfigWithUpgrades(text string, curioConfigWithDefaults *config.CurioCo
 	return meta, err
 }
 func GetConfig(ctx context.Context, layers []string, db *harmonydb.DB) (*config.CurioConfig, error) {
+	err := updateBaseLayer(ctx, db)
+	if err != nil {
+		return nil, err
+	}
+
 	curioConfig := config.DefaultCurioConfig()
 	have := []string{}
 	layers = append([]string{"base"}, layers...) // Always stack on top of "base" layer
@@ -462,6 +468,131 @@ func GetConfig(ctx context.Context, layers []string, db *harmonydb.DB) (*config.
 	return curioConfig, nil
 }
 
+func updateBaseLayer(ctx context.Context, db *harmonydb.DB) error {
+	_, err := db.BeginTransaction(ctx, func(tx *harmonydb.Tx) (commit bool, err error) {
+		// Get existing base from DB
+		text := ""
+		err = tx.QueryRow(`SELECT config FROM harmony_config WHERE title=$1`, "base").Scan(&text)
+		if err != nil {
+			if strings.Contains(err.Error(), sql.ErrNoRows.Error()) {
+				return false, fmt.Errorf("missing layer 'base' ")
+			}
+			return false, fmt.Errorf("could not read layer 'base': %w", err)
+		}
+
+		// Load the existing configuration
+		cfg := config.DefaultCurioConfig()
+		metadata, err := LoadConfigWithUpgrades(text, cfg)
+		if err != nil {
+			return false, fmt.Errorf("could not read base layer, bad toml %s: %w", text, err)
+		}
+
+		// Capture unknown fields
+		keys := removeUnknownEntries(metadata.Keys(), metadata.Undecoded())
+		unrecognizedFields := extractUnknownFields(keys, text)
+
+		// Convert the updated config back to TOML string
+		cb, err := config.ConfigUpdate(cfg, config.DefaultCurioConfig(), config.Commented(true), config.DefaultKeepUncommented(), config.NoEnv())
+		if err != nil {
+			return false, xerrors.Errorf("cannot update base config: %w", err)
+		}
+
+		// Merge unknown fields back into the updated config
+		finalConfig, err := mergeUnknownFields(string(cb), unrecognizedFields)
+		if err != nil {
+			return false, xerrors.Errorf("cannot merge unknown fields: %w", err)
+		}
+
+		// Check if we need to update the DB
+		if text == finalConfig {
+			return false, nil
+		}
+
+		// Save the updated base with merged comments
+		_, err = tx.Exec("UPDATE harmony_config SET config=$1 WHERE title='base'", finalConfig)
+		if err != nil {
+			return false, xerrors.Errorf("cannot update base config: %w", err)
+		}
+
+		return true, nil
+	}, harmonydb.OptionRetry())
+
+	if err != nil {
+		return err
+	}
+
+	return nil
+}
+
+func extractUnknownFields(knownKeys []toml.Key, originalConfig string) map[string]interface{} {
+	// Parse the original config into a raw map
+	var rawConfig map[string]interface{}
+	err := toml.Unmarshal([]byte(originalConfig), &rawConfig)
+	if err != nil {
+		log.Warnw("Failed to parse original config for unknown fields", "error", err)
+		return nil
+	}
+
+	// Collect all recognized keys
+	recognizedKeys := map[string]struct{}{}
+	for _, key := range knownKeys {
+		recognizedKeys[strings.Join(key, ".")] = struct{}{}
+	}
+
+	// Identify unrecognized fields
+	unrecognizedFields := map[string]interface{}{}
+	for key, value := range rawConfig {
+		if _, recognized := recognizedKeys[key]; !recognized {
+			unrecognizedFields[key] = value
+		}
+	}
+	return unrecognizedFields
+}
+
+func removeUnknownEntries(array1, array2 []toml.Key) []toml.Key {
+	// Create a set from array2 for fast lookup
+	toRemove := make(map[string]struct{}, len(array2))
+	for _, key := range array2 {
+		toRemove[key.String()] = struct{}{}
+	}
+
+	// Filter array1, keeping only elements not in toRemove
+	var result []toml.Key
+	for _, key := range array1 {
+		if _, exists := toRemove[key.String()]; !exists {
+			result = append(result, key)
+		}
+	}
+
+	return result
+}
+
+func mergeUnknownFields(updatedConfig string, unrecognizedFields map[string]interface{}) (string, error) {
+	// Parse the updated config into a raw map
+	var updatedConfigMap map[string]interface{}
+	err := toml.Unmarshal([]byte(updatedConfig), &updatedConfigMap)
+	if err != nil {
+		return "", fmt.Errorf("failed to parse updated config: %w", err)
+	}
+
+	// Merge unrecognized fields
+	for key, value := range unrecognizedFields {
+		if _, exists := updatedConfigMap[key]; !exists {
+			updatedConfigMap[key] = value
+		}
+	}
+
+	// Convert back into TOML
+	b := new(bytes.Buffer)
+	encoder := toml.NewEncoder(b)
+	err = encoder.Encode(updatedConfigMap)
+	if err != nil {
+		return "", fmt.Errorf("failed to marshal final config: %w", err)
+	}
+
+	return b.String(), nil
+}
+
 func GetDefaultConfig(comment bool) (string, error) {
 	c := config.DefaultCurioConfig()
 	cb, err := config.ConfigUpdate(c, nil, config.Commented(comment), config.DefaultKeepUncommented(), config.NoEnv())
diff --git a/deps/deps_test.go b/deps/deps_test.go
new file mode 100644
index 000000000..5cec4b5a4
--- /dev/null
+++ b/deps/deps_test.go
@@ -0,0 +1,124 @@
+package deps
+
+import (
+	"bytes"
+	"testing"
+
+	"github.com/BurntSushi/toml"
+)
+
+type ExampleConfig struct {
+	Subsystems struct {
+		EnableWindowPost   bool
+		WindowPostMaxTasks int
+	}
+	Fees struct {
+		DefaultMaxFee string
+	}
+}
+
+// An original TOML configuration that has both recognized and unknown fields.
+const originalTOML = `
+[Subsystems]
+  EnableWindowPost = true
+  WindowPostMaxTasks = 5
+
+[Fees]
+  DefaultMaxFee = "0.07 FIL"
+
+[UnknownSection]
+  SomeUnknownKey = "whatever"
+  AnotherField   = 123
+
+[AnotherUnknownSection.Nested]
+  NestedValue = "I am nested"
+`
+
+func TestExtractAndMergeUnknownFields(t *testing.T) {
+	//----------------------------------------------------------------------
+	// Step 1: Decode original TOML into recognized struct & collect MetaData
+	//----------------------------------------------------------------------
+	var recognized ExampleConfig
+	meta, err := toml.Decode(originalTOML, &recognized)
+	if err != nil {
+		t.Fatalf("failed to decode recognized fields: %v", err)
+	}
+
+	keys := removeUnknownEntries(meta.Keys(), meta.Undecoded())
+
+	//----------------------------------------------------------------------
+	// Step 2: Extract the unknown fields using extractUnknownFields
+	//----------------------------------------------------------------------
+	unknownFields := extractUnknownFields(keys, originalTOML)
+	if len(unknownFields) == 0 {
+		t.Errorf("expected unknown fields, got none")
+	}
+
+	//----------------------------------------------------------------------
+	// Step 3: Update recognized fields in the struct
+	//----------------------------------------------------------------------
+	recognized.Subsystems.EnableWindowPost = false // flip the boolean
+	recognized.Subsystems.WindowPostMaxTasks = 10  // change from 5 to 10
+	recognized.Fees.DefaultMaxFee = "0.08 FIL"     // update the fee
+
+	//----------------------------------------------------------------------
+	// Step 4: Re-encode recognized fields back to TOML
+	//----------------------------------------------------------------------
+	var buf bytes.Buffer
+	if err := toml.NewEncoder(&buf).Encode(recognized); err != nil {
+		t.Fatalf("failed to marshal updated recognized config: %v", err)
+	}
+	updatedConfig := buf.String()
+
+	//----------------------------------------------------------------------
+	// Step 5: Merge unknown fields back
+	//----------------------------------------------------------------------
+	finalConfig, err := mergeUnknownFields(updatedConfig, unknownFields)
+	if err != nil {
+		t.Fatalf("failed to merge unknown fields: %v", err)
+	}
+
+	//----------------------------------------------------------------------
+	// Assertions: Check recognized fields have changed & unknown remain
+	//----------------------------------------------------------------------
+	// 5a. Parse final config into a map to check contents
+	var finalMap map[string]interface{}
+	if err := toml.Unmarshal([]byte(finalConfig), &finalMap); err != nil {
+		t.Fatalf("failed to parse final config: %v\nFinal Config:\n%s", err, finalConfig)
+	}
+
+	// 5b. Check recognized fields updated
+	subsystems, ok := finalMap["Subsystems"].(map[string]interface{})
+	if !ok {
+		t.Fatalf("expected 'Subsystems' in final config")
+	}
+
+	if enable, _ := subsystems["EnableWindowPost"].(bool); enable {
+		t.Errorf("expected Subsystems.EnableWindowPost = false, got true")
+	}
+	if tasks, _ := subsystems["WindowPostMaxTasks"].(int64); tasks != 10 {
+		t.Errorf("expected Subsystems.WindowPostMaxTasks = 10, got %d", tasks)
+	}
+
+	fees, ok := finalMap["Fees"].(map[string]interface{})
+	if !ok {
+		t.Fatalf("expected 'Fees' in final config")
+	}
+	if defaultFee, _ := fees["DefaultMaxFee"].(string); defaultFee != "0.08 FIL" {
+		t.Errorf("expected Fees.DefaultMaxFee = '0.08 FIL', got '%s'", defaultFee)
+	}
+
+	// 5c. Check unknown fields remain
+	if _, exists := finalMap["UnknownSection"]; !exists {
+		t.Errorf("expected UnknownSection to remain in final config, but not found")
+	}
+	if anotherUnknown, exists := finalMap["AnotherUnknownSection"]; !exists {
+		t.Errorf("expected AnotherUnknownSection to remain in final config, but not found")
+	} else {
+		// Inside nested
+		nested := anotherUnknown.(map[string]interface{})["Nested"].(map[string]interface{})
+		if val, ok := nested["NestedValue"].(string); !ok || val != "I am nested" {
+			t.Errorf("expected AnotherUnknownSection.Nested.NestedValue = 'I am nested', got '%v'", val)
+		}
+	}
+}