diff --git a/CMakeLists.txt b/CMakeLists.txt
index 08f774c168ac..7c9b9f35051f 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -824,7 +824,7 @@ add_subdirectory(Source)
 # Install shared data files
 #
 if(NOT CMAKE_SYSTEM_NAME MATCHES "Darwin|Windows")
-  install(DIRECTORY Data/Sys/ DESTINATION ${datadir}/sys PATTERN)
+  install(DIRECTORY Data/Sys/ DESTINATION ${datadir}/Sys PATTERN)
   install(DIRECTORY Data/user/ DESTINATION ${datadir}/user PATTERN)
 endif()
 if(NOT CMAKE_SYSTEM_NAME MATCHES "Linux|FreeBSD|OpenBSD|Darwin")
diff --git a/Distribution/flatpak/flatpak.yml b/Distribution/flatpak/flatpak.yml
index 3bd72a396992..e1c5e0247a2c 100644
--- a/Distribution/flatpak/flatpak.yml
+++ b/Distribution/flatpak/flatpak.yml
@@ -99,6 +99,10 @@ modules:
 
   - name: project-plus-dolphin
     buildsystem: cmake-ninja
+    # Build out of tree; an in-source build writes CMake files into the submodule checkouts,
+    # which makes `git describe --dirty` add "-dirty" to the version string.
+    # Note: commands below (post-install) run from the _flatpak_build subdirectory.
+    builddir: true
     config-opts:
       - -DCMAKE_BUILD_TYPE=Release
       - -DENABLE_ALSA=OFF
@@ -156,15 +160,15 @@ modules:
       #  dest-filename: project-plus-dolphin-wrapper
     post-install:
       - |
-      - install -D -t ${FLATPAK_DEST}/bin/ project-plus-dolphin-wrapper.sh
+      - install -D -t ${FLATPAK_DEST}/bin/ ../project-plus-dolphin-wrapper.sh
       - desktop-file-edit --set-key=Exec --set-value='/app/bin/project-plus-dolphin-wrapper.sh'
         /app/share/applications/project-plus-dolphin.desktop
       - desktop-file-edit --set-key=Name --set-value='Project Plus Dolphin'
         /app/share/applications/project-plus-dolphin.desktop
-      - rm -r ${FLATPAK_DEST}/share/project-plus-dolphin/sys                                                                                       # Remove preinstalled sys directory
-      - mv Data/Sys ${FLATPAK_DEST}/share/project-plus-dolphin/sys/                                                                                # Move Sys directory to correct location (only use without the -DLINUX_LOCAL_DEV=true flag set
+      - rm -r ${FLATPAK_DEST}/share/project-plus-dolphin/Sys                                                                                       # Remove preinstalled Sys directory
+      - mv ../Data/Sys ${FLATPAK_DEST}/share/project-plus-dolphin/Sys/                                                                                # Move Sys directory to correct location (only use without the -DLINUX_LOCAL_DEV=true flag set
       #- tar --transform="s|sd.raw|WiiSD.raw|" -xf sd.tar.gz -C ${FLATPAK_DEST}/share/project-plus-dolphin/user/Wii/                               # Extract, rename and move SD card to correct location
-      #- mv Launcher ${FLATPAK_DEST}/share/project-plus-dolphin/sys/Wii/                                                                            # Move Launcher directory to correct location
-      #- mkdir -p ${FLATPAK_DEST}/share/project-plus-dolphin/sys/Load/Textures                                                                      # Make directory for HD textures
-      #- mv "ModPack/Full Quality HD Textures" ${FLATPAK_DEST}/share/project-plus-dolphin/sys/Load/Textures/RSBE01/                              	  # Move HD Textures from ModPack to correct location
-      - install -Dm644 org.projectplusgame.project-plus-dolphin.metainfo.xml -t ${FLATPAK_DEST}/share/metainfo/                                    # Install metainfo file
+      #- mv Launcher ${FLATPAK_DEST}/share/project-plus-dolphin/Sys/Wii/                                                                            # Move Launcher directory to correct location
+      #- mkdir -p ${FLATPAK_DEST}/share/project-plus-dolphin/Sys/Load/Textures                                                                      # Make directory for HD textures
+      #- mv "ModPack/Full Quality HD Textures" ${FLATPAK_DEST}/share/project-plus-dolphin/Sys/Load/Textures/RSBE01/                              	  # Move HD Textures from ModPack to correct location
+      - install -Dm644 ../org.projectplusgame.project-plus-dolphin.metainfo.xml -t ${FLATPAK_DEST}/share/metainfo/                                    # Install metainfo file
diff --git a/Distribution/flatpak/project-plus-dolphin-wrapper.sh b/Distribution/flatpak/project-plus-dolphin-wrapper.sh
index d7746dcd02a8..26c2cf974039 100644
--- a/Distribution/flatpak/project-plus-dolphin-wrapper.sh
+++ b/Distribution/flatpak/project-plus-dolphin-wrapper.sh
@@ -13,7 +13,7 @@ echo "Make directory /var/config/project-plus-dolphin if it doesn't exist"
 mkdir -p /var/config/project-plus-dolphin
 
 # Create and set variables for the system and user SD card creation dates
-# SystemSDCardCreationDate=`stat --format="%W" /app/share/project-plus-dolphin/sys/Load/WiiSD.raw`
+# SystemSDCardCreationDate=`stat --format="%W" /app/share/project-plus-dolphin/Sys/Load/WiiSD.raw`
 # UserSDCardCreationDate=`stat --format="%W" /var/data/project-plus-dolphin/Load/WiiSD.raw`
 
 # echo "Check if there is a newer SD card version"
@@ -23,19 +23,19 @@ mkdir -p /var/config/project-plus-dolphin
 #     mkdir -p /var/data/project-plus-dolphin/Load
 
 #     echo "Copy newer SD card to user data directory"
-#     cp /app/share/project-plus-dolphin/sys/Load/WiiSD.raw /var/data/project-plus-dolphin/Load/WiiSD.raw
+#     cp /app/share/project-plus-dolphin/Sys/Load/WiiSD.raw /var/data/project-plus-dolphin/Load/WiiSD.raw
 # else
 #     echo "SD card is already at latest version"
 # fi
 
 echo "Copy dol files to user data directory if they don't already exist"
-cp -nr /app/share/project-plus-dolphin/sys/Wii/Launcher /var/data/project-plus-dolphin/user/Wii/
+cp -nr /app/share/project-plus-dolphin/Sys/Wii/Launcher /var/data/project-plus-dolphin/user/Wii/
 
 echo "Copy user directory to Flatpak user data directory (Overwritting any files already there with any newer files)"
 cp -ru /app/share/project-plus-dolphin/user /var/data/project-plus-dolphin/
 
 # Create and set variables for the system and user HD textures creation dates
-SystemHDTexturesCreationDate=`stat --format="%W" /app/share/project-plus-dolphin/sys/Load/Textures/RSBE01`
+SystemHDTexturesCreationDate=`stat --format="%W" /app/share/project-plus-dolphin/Sys/Load/Textures/RSBE01`
 UserHDTexturesCreationDate=`stat --format="%W" /var/data/project-plus-dolphin/user/Load/Textures/RSBE01`
 
 echo "Check if there are newer HD textures"
@@ -45,7 +45,7 @@ then
     mkdir -p /var/data/project-plus-dolphin/Load/Textures
 
     echo "Copy newer HD textures to user data directory"
-    cp -r /app/share/project-plus-dolphin/sys/Load/Textures/RSBE01 /var/data/project-plus-dolphin/user/Load/Textures
+    cp -r /app/share/project-plus-dolphin/Sys/Load/Textures/RSBE01 /var/data/project-plus-dolphin/user/Load/Textures
 else
     echo "HD textures are already at latest version"
 fi
diff --git a/Source/Core/Common/FileUtil.cpp b/Source/Core/Common/FileUtil.cpp
index 5358619525a1..bb5536e9ca77 100644
--- a/Source/Core/Common/FileUtil.cpp
+++ b/Source/Core/Common/FileUtil.cpp
@@ -777,6 +777,8 @@ static std::string CreateSysDirectoryPath()
   const std::string local_sys_directory = GetExeDirectory() + DIR_SEP SYS_FOLDER_NAME DIR_SEP;
   if (IsDirectory(local_sys_directory))
     sys_directory = local_sys_directory;
+  else if (!IsDirectory(SYSDATA_DIR) && IsDirectory(DATA_DIR "sys"))
+    sys_directory = DATA_DIR "sys" DIR_SEP;  // Installs packaged before the Sys rename
   else
     sys_directory = SYSDATA_DIR DIR_SEP;
 
diff --git a/Source/Core/Core/WiiRoot.cpp b/Source/Core/Core/WiiRoot.cpp
index e2ea0a6db1ab..4d59e635bd5b 100644
--- a/Source/Core/Core/WiiRoot.cpp
+++ b/Source/Core/Core/WiiRoot.cpp
@@ -221,7 +221,11 @@ void InitializeWiiRoot(bool use_temporary)
     MoveToBackupIfExists(s_temp_redirect_root);
 
     File::SetUserPath(D_SESSION_WIIROOT_IDX, s_temp_wii_root);
-	File::Copy(File::GetSysDirectory() + NETPLAY_SAVE_DIR, s_temp_wii_root);
+    const std::string netplay_save_dir = File::GetSysDirectory() + NETPLAY_SAVE_DIR;
+    if (!File::IsDirectory(netplay_save_dir))
+      ERROR_LOG_FMT(IOS_FS, "NetPlay save directory {} is missing", netplay_save_dir);
+    else if (!File::Copy(netplay_save_dir, s_temp_wii_root))
+      ERROR_LOG_FMT(IOS_FS, "Failed to copy NetPlay save from {}", netplay_save_dir);
   }
   else
   {