diff --git a/src/citron/main.cpp b/src/citron/main.cpp
index 86b7e9251..534bb97eb 100644
--- a/src/citron/main.cpp
+++ b/src/citron/main.cpp
@@ -2308,6 +2308,13 @@ void GMainWindow::OnEmulationStopped() {
 
     emulation_running = false;
 
+    // Reset the startup sync flag for the next session.
+    has_performed_initial_sync = false;
+    LOG_INFO(Frontend, "Mirroring: Emulation stopped. Re-arming startup sync for next game list refresh.");
+
+    // This is necessary to reset the in-memory state for the next launch.
+    system->GetFileSystemController().CreateFactories(*vfs, true);
+
     discord_rpc->Update();
 
 #ifdef __unix__
@@ -2426,30 +2433,28 @@ void GMainWindow::OnGameListOpenFolder(u64 program_id, GameListOpenTarget target
     case GameListOpenTarget::SaveData: {
         open_target = tr("Save Data");
 
-        // 1. Check for Mirrored Path FIRST (opens the external directory)
+        // 1. Priority 1: Mirrored Path (opens the external directory)
         if (Settings::values.mirrored_save_paths.count(program_id)) {
             const std::string& mirrored_path_str =
                 Settings::values.mirrored_save_paths.at(program_id);
             if (!mirrored_path_str.empty() && Common::FS::IsDir(mirrored_path_str)) {
-                LOG_INFO(Frontend, "Opening mirrored save data path for program_id={:016x}",
+                LOG_INFO(Frontend, "Opening external mirrored save data path for program_id={:016x}",
                          program_id);
                 QDesktopServices::openUrl(
                     QUrl::fromLocalFile(QString::fromStdString(mirrored_path_str)));
                 return;
             }
         }
-        // 2. Check for Per-Game Custom Path
+        // 2. Priority 2: Per-Game Custom Path
         else if (Settings::values.custom_save_paths.count(program_id)) {
             const std::string& custom_path_str = Settings::values.custom_save_paths.at(program_id);
             if (!custom_path_str.empty() && Common::FS::IsDir(custom_path_str)) {
-                LOG_INFO(Frontend, "Opening custom save data path for program_id={:016x}",
-                         program_id);
-                QDesktopServices::openUrl(
-                    QUrl::fromLocalFile(QString::fromStdString(custom_path_str)));
+                LOG_INFO(Frontend, "Opening per-game custom save data path for program_id={:016x}", program_id);
+                QDesktopServices::openUrl(QUrl::fromLocalFile(QString::fromStdString(custom_path_str)));
                 return;
             }
         }
-        // 3. Check for Global Custom Save Path
+        // 3. Priority 3: Global Custom Path
         else if (Settings::values.global_custom_save_path_enabled.GetValue()) {
             const std::string& global_path_str =
                 Settings::values.global_custom_save_path.GetValue();