diff --git a/server/server-config/src/main/kotlin/suwayomi/tachidesk/server/ServerConfig.kt b/server/server-config/src/main/kotlin/suwayomi/tachidesk/server/ServerConfig.kt
index c2e5fe21f..a922334f9 100644
--- a/server/server-config/src/main/kotlin/suwayomi/tachidesk/server/ServerConfig.kt
+++ b/server/server-config/src/main/kotlin/suwayomi/tachidesk/server/ServerConfig.kt
@@ -290,7 +290,7 @@ class ServerConfig(
                     @Suppress("UNCHECKED_CAST")
                     (it.unwrapped() as? List<String>)
                         ?.map {
-                            if (it.contains("github")) {
+                            if (it.contains("github.com")) {
                                 it.replace(repoMatchRegex) {
                                     "https://raw.githubusercontent.com/${it.groupValues[2]}/${it.groupValues[3]}/" +
                                         (it.groupValues.getOrNull(4)?.ifBlank { null } ?: "repo") +
@@ -304,7 +304,7 @@ class ServerConfig(
                 },
             ),
         readMigrated = { extensionStores.value },
-        setMigrated = { extensionStores.value = it },
+        setMigrated = { extensionStores.value = (extensionStores.value + it).distinct() },
         typeInfo =
             SettingsRegistry.PartialTypeInfo(
                 specificType = "List<String>",
@@ -1118,7 +1118,7 @@ class ServerConfig(
     val extensionStores: MutableStateFlow<List<String>> by ListSetting<String>(
         protoNumber = 97,
         group = SettingGroup.EXTENSION,
-        privacySafe = false,
+        privacySafe = true,
         defaultValue = emptyList(),
         itemValidator = { url ->
             if (url.isNotEmpty()) {
@@ -1128,11 +1128,7 @@ class ServerConfig(
             }
         },
         itemToValidValue = { url ->
-            if (url.isNotEmpty()) {
-                url
-            } else {
-                null
-            }
+            url.ifEmpty { null }
         },
         typeInfo =
             SettingsRegistry.PartialTypeInfo(
diff --git a/server/src/main/kotlin/suwayomi/tachidesk/manga/impl/extension/ExtensionStoreService.kt b/server/src/main/kotlin/suwayomi/tachidesk/manga/impl/extension/ExtensionStoreService.kt
index 2eac26d5e..80be16f25 100644
--- a/server/src/main/kotlin/suwayomi/tachidesk/manga/impl/extension/ExtensionStoreService.kt
+++ b/server/src/main/kotlin/suwayomi/tachidesk/manga/impl/extension/ExtensionStoreService.kt
@@ -134,7 +134,7 @@ object ExtensionStoreService {
                     transaction {
                         ExtensionStoreTable.deleteWhere { ExtensionStoreTable.indexUrl eq oldIndexUrl }
                     }
-                    syncDbToPrefs()
+                    syncDbToPrefs(oldIndexUrl)
                 }
                 store
             } catch (e: Exception) {
@@ -144,7 +144,7 @@ object ExtensionStoreService {
         }
     }
 
-    fun syncDbToPrefs() {
+    fun syncDbToPrefs(keepRemoved: String? = null) {
         val dbStores =
             transaction {
                 ExtensionStoreTable
@@ -154,8 +154,8 @@ object ExtensionStoreService {
             }
 
         val currentPrefs = serverConfig.extensionStores.value.toSet()
-        val toAdd = dbStores - currentPrefs
-        val toRemove = currentPrefs - dbStores
+        val toAdd = (dbStores - currentPrefs - keepRemoved).filterNotNull()
+        val toRemove = (currentPrefs - dbStores + keepRemoved).filterNotNull()
 
         if (toAdd.isNotEmpty()) {
             serverConfig.extensionStores.value = (serverConfig.extensionStores.value + toAdd).distinct()
@@ -180,6 +180,12 @@ object ExtensionStoreService {
             try {
                 val store = fetch(url)
                 upsert(store)
+                if (store.indexUrl != url) {
+                    transaction {
+                        ExtensionStoreTable.deleteWhere { ExtensionStoreTable.indexUrl eq url }
+                    }
+                    syncDbToPrefs(url)
+                }
             } catch (e: Exception) {
                 logger.warn(e) { "Failed to sync preference store '$url' to database" }
             }
diff --git a/server/src/main/kotlin/suwayomi/tachidesk/server/ServerSetup.kt b/server/src/main/kotlin/suwayomi/tachidesk/server/ServerSetup.kt
index ea77725a4..a14fb27eb 100644
--- a/server/src/main/kotlin/suwayomi/tachidesk/server/ServerSetup.kt
+++ b/server/src/main/kotlin/suwayomi/tachidesk/server/ServerSetup.kt
@@ -525,6 +525,7 @@ fun applicationSetup() {
         serverConfig.extensionStores,
         { _ ->
             ExtensionStoreService.syncPrefsToDb()
+            ExtensionStoreService.syncDbToPrefs()
         },
         ignoreInitialValue = false,
     )