I think this might be happening because globals.buildSystem doesn't notice new files? Anyways, this seems good to track. I'll try to fix in the next few days.

Steps to Reproduce

1. Create new Flutter project flutter create hot_reload_bug.
2. Create empty l10n.yaml or cd hot_reload_bug && touch l10n.yaml.
3. Add the following to pubspec.yaml:

dependencies:
  flutter:
    sdk: flutter
  flutter_localizations: # Add this line
    sdk: flutter         # Add this line
  intl: ^0.17.0 # Add this line
...
flutter:
  generate: true # Add this line

4. Add a file lib/l10n/app_en.arb with

{
    "@@locale": "en",
    "helloWorld": "Hello World!",
    "@helloWorld": {
      "description": "The conventional newborn programmer greeting"
    }
}

5. Run the app with flutter run. This will generate .flutter_tool/flutter_gen/gen_l10n/app_localizations.
6. Add a new file app_es.arb with

{
    "@@locale": "es",
    "helloWorld": "¡Hola Mundo!"
}
7. Hot reload. This will not generate a new file for Spanish.

Expected Behavior

Creating a new .arb file and hot reloading should cause localizations to be regenerated.