Hey @farfromrefug ,
I've transferred this issue to android-runtime repository as the problem is only for Android. NativeScript CLI detects the change in the native-api-usage.json file and triggers native build, but it seems some of the gradle tasks are not executed in this case.
Steps to reproduce:

tns create myApp --js
cd myApp
touch app/App_Resources/Android/native-api-usage.json
echo '{ "whitelist":["java.util:List"] }' > app/App_Resources/Android/native-api-usage.json
tns run android --justlaunch # app will fail at runtime
echo '{ }' > app/App_Resources/Android/native-api-usage.json
tns run android --justlaunch # app should work, but it still fails at runtime
rm -rf platforms
tns run android --justlaunch # app will work

NOTE: The issue will be reproduced even if you use tns run android and change the native-api-usage.json file.

@rosen-vladimirov exactly what i am seeing!
Thanks

I made a simple change in the build.gradle of the apps and this should do the trick to run the buildMetadata task. I linked a PR here. I'll test it properly tomorrow as it's getting late now.