For the installer it's a bit different, because the default folders default to Reloaded's directory.

But in this case, you may actually also want to check the Mods folder location from the LoaderConfig (get it via IoC if needed).

The user can technically remap the mods folder location via the LoaderConfig's .json in AppData.

The actual problematic folder is the Mods folder after all.

The actual problematic folder is the Mods folder after all.

In the case of a real user, the crash was occurring in the Bootstrapper.dll - so I wouldn't just want to check the Mods folder

I poorly worded it by forgetting to remove 'instead' at the end. I meant to say 'in addition'.

I just tried moving the folder and seeing what changed in the config.
Everything updates once you close Reloaded-II:

  "LoaderPath32": "C:\\Games\\OneDrive\\Launcher\\Loader\\x86\\Reloaded.Mod.Loader.dll",
  "LoaderPath64": "C:\\Games\\OneDrive\\Launcher\\Loader\\x64\\Reloaded.Mod.Loader.dll",
  "LauncherPath": "C:\\Games\\OneDrive\\Launcher\\Reloaded-II.exe",
  "Bootstrapper32Path": "C:\\Games\\OneDrive\\Launcher\\Loader\\x86\\Bootstrapper\\Reloaded.Mod.Loader.Bootstrapper.dll",
  "Bootstrapper64Path": "C:\\Games\\OneDrive\\Launcher\\Loader\\x64\\Bootstrapper\\Reloaded.Mod.Loader.Bootstrapper.dll",
  "ApplicationConfigDirectory": "C:\\Games\\OneDrive\\Launcher\\Apps",
  "ModUserConfigDirectory": "C:\\Games\\OneDrive\\Launcher\\User\\Mods",
  "MiscConfigDirectory": "C:\\Games\\OneDrive\\Launcher\\User\\Misc",
  "PluginConfigDirectory": "C:\\Games\\OneDrive\\Launcher\\Plugins",
  "ModConfigDirectory": "C:\\Games\\OneDrive\\Launcher\\Mods",
  "EnabledPlugins": [],
  "LanguageFile": "C:\\Games\\OneDrive\\Launcher\\\\Assets\\Languages\\en-GB.xaml",
  "ThemeFile": "C:\\Games\\OneDrive\\Launcher\\\\Theme\\Default.xaml",

I don't really see a point to check for a custom edited \Mods folder, since there's no flow in the UI to edit this.
If a user is editing this file I think its fine to not warn them since they are an advanced user.

The config paths reset if the locations they point to are invalid. If they are valid, they are used.

A user may opt to move their folder while the program is closed and then edit the .json before starting the program again. That should work/be recognised.

Note the config is written to on window close, hence the need to change after closing.

Added:

Which only will be checked if the R-II path check passes.