The issue look like the Android Studio problem, and submit to Android Studio team, not anrdoid-ndk group, I think. It would be helped if you can show the Android Studio version, plugin and how do you debug your app, with clear information, we might give you some advices.
I am not in Google team, however, I also use Android Studio to debug native code, and it works. So I might give you some advices if you give the information below.
Cheers