diff --git a/src/core/system.cpp b/src/core/system.cpp
index 91464f17b..11f1ce804 100644
--- a/src/core/system.cpp
+++ b/src/core/system.cpp
@@ -1323,9 +1323,10 @@ void System::UpdateFolderPaths()
     return;
   }
 
-  const std::string old_gamesettings(EmuFolders::GameSettings);
-  const std::string old_inputprofiles(EmuFolders::InputProfiles);
-  const std::string old_memorycards(EmuFolders::MemoryCards);
+  const std::string old_cheats = EmuFolders::Cheats;
+  const std::string old_gamesettings = EmuFolders::GameSettings;
+  const std::string old_inputprofiles = EmuFolders::InputProfiles;
+  const std::string old_memorycards = EmuFolders::MemoryCards;
 
   // have to manually grab the lock here, because of the ReloadGameSettings() below.
   {
@@ -1337,7 +1338,17 @@ void System::UpdateFolderPaths()
   if (IsValid())
   {
     if (old_gamesettings != EmuFolders::GameSettings && UpdateGameSettingsLayer())
+    {
+      if (!IsReplayingGPUDump())
+        Cheats::ReloadCheats(old_cheats != EmuFolders::Cheats, true, false, true, false);
+
       ApplySettings(false);
+    }
+    else if (old_cheats != EmuFolders::Cheats)
+    {
+      if (!IsReplayingGPUDump())
+        Cheats::ReloadCheats(true, false, false, true, false);
+    }
 
     if (!s_state.input_profile_name.empty() && old_inputprofiles != EmuFolders::InputProfiles)
     {
@@ -1422,7 +1433,7 @@ bool System::GetGameSettingsInterface(INISettingsInterface* sif, const GameDatab
               ERROR_LOG("Failed to parse separate disc game settings ini '{}': {}", Path::GetFileName(sif->GetPath()),
                         error.GetDescription());
 
-              sif->Clear();
+              sif->ClearContentsAndDirty(true);
               return false;
             }
           }
@@ -1433,7 +1444,7 @@ bool System::GetGameSettingsInterface(INISettingsInterface* sif, const GameDatab
                              Path::GetFileName(sif->GetPath()));
 
             // return empty ini struct?
-            sif->Clear();
+            sif->ClearContentsAndDirty(true);
             return false;
           }
         }
@@ -1444,7 +1455,7 @@ bool System::GetGameSettingsInterface(INISettingsInterface* sif, const GameDatab
       ERROR_LOG("Failed to parse game settings ini '{}': {}", Path::GetFileName(sif->GetPath()),
                 error.GetDescription());
 
-      sif->Clear();
+      sif->ClearContentsAndDirty(true);
       return false;
     }
   }
@@ -1454,7 +1465,7 @@ bool System::GetGameSettingsInterface(INISettingsInterface* sif, const GameDatab
       INFO_COLOR_LOG(StrongCyan, "No game settings found (tried '{}')", Path::GetFileName(sif->GetPath()));
 
     // return empty ini struct?
-    sif->Clear();
+    sif->ClearContentsAndDirty(true);
     return false;
   }
 
@@ -1520,15 +1531,13 @@ void System::UpdateInputSettingsLayer(std::string input_profile_name, std::uniqu
       {
         ERROR_LOG("Failed to parse input profile ini '{}': {}",
                   Path::GetFileName(s_state.input_settings_interface.GetPath()), error.GetDescription());
-        s_state.input_settings_interface.ClearPathAndContents();
-        input_profile_name = {};
+        s_state.input_settings_interface.ClearContentsAndDirty(true);
       }
     }
     else
     {
       WARNING_LOG("No input profile found (tried '{}')", Path::GetFileName(s_state.input_settings_interface.GetPath()));
-      s_state.input_settings_interface.ClearPathAndContents();
-      input_profile_name = {};
+      s_state.input_settings_interface.ClearContentsAndDirty(true);
     }
   }
   else
diff --git a/src/duckstation-qt/controllersettingswindow.cpp b/src/duckstation-qt/controllersettingswindow.cpp
index 84ff70a12..442ad9e8f 100644
--- a/src/duckstation-qt/controllersettingswindow.cpp
+++ b/src/duckstation-qt/controllersettingswindow.cpp
@@ -116,8 +116,8 @@ ControllerSettingsWindow* ControllerSettingsWindow::editControllerSettingsForGam
   dlg->setWindowFlag(Qt::Window);
   dlg->setAttribute(Qt::WA_DeleteOnClose);
   dlg->setWindowModality(Qt::WindowModal);
-  dlg->setWindowTitle(parent->windowTitle());
-  dlg->setWindowIcon(parent->windowIcon());
+  dlg->setWindowTitle(parent->window()->windowTitle());
+  dlg->setWindowIcon(parent->window()->windowIcon());
   dlg->show();
   return dlg;
 }
diff --git a/src/duckstation-qt/gamesummarywidget.cpp b/src/duckstation-qt/gamesummarywidget.cpp
index 977ae4298..0d1db1688 100644
--- a/src/duckstation-qt/gamesummarywidget.cpp
+++ b/src/duckstation-qt/gamesummarywidget.cpp
@@ -314,6 +314,16 @@ void GameSummaryWidget::onSeparateDiscSettingsChanged(Qt::CheckState state)
     m_dialog->setBoolSettingValue("Main", "UseSeparateConfigForDiscSet", true);
   else
     m_dialog->removeSettingValue("Main", "UseSeparateConfigForDiscSet");
+
+  // Need to update for all discs when clearing separate-disc-settings.
+  if (state == Qt::Unchecked)
+  {
+    for (const std::string_view& serial : m_dialog->getDatabaseEntry()->disc_set->serials)
+    {
+      if (serial != m_dialog->getGameSerial())
+        System::ReloadSettingsForPath(System::GetGameSettingsPath(serial, true));
+    }
+  }
 }
 
 void GameSummaryWidget::onChangeSerialClicked()
diff --git a/src/util/ini_settings_interface.cpp b/src/util/ini_settings_interface.cpp
index 55c87c3b3..01c88c433 100644
--- a/src/util/ini_settings_interface.cpp
+++ b/src/util/ini_settings_interface.cpp
@@ -426,6 +426,12 @@ void INISettingsInterface::Clear(bool clear_memory /* = false */)
   }
 }
 
+void INISettingsInterface::ClearContentsAndDirty(bool clear_memory)
+{
+  Clear(clear_memory);
+  m_dirty = false;
+}
+
 void INISettingsInterface::ClearPathAndContents()
 {
   Clear(true);
diff --git a/src/util/ini_settings_interface.h b/src/util/ini_settings_interface.h
index 6f0988398..e787abc59 100644
--- a/src/util/ini_settings_interface.h
+++ b/src/util/ini_settings_interface.h
@@ -51,6 +51,7 @@ public:
   std::string SaveToString(SectionSaveOrder save_order = {}) const;
 
   void Clear(bool clear_memory = false);
+  void ClearContentsAndDirty(bool clear_memory);
   void ClearPathAndContents();
   void CompactStrings();