Hi Vincent, I got the same error when I upgraded my project. You can solve this by adding the missing js file yourself.
From your phonegap folder go to node_modules/@mendix/mendix-hybrid-app-base Then create new scripts folder.
Then create new before_build.js file with the following content:
#!/usr/bin/env node
require('fs').copyFileSync("./config/build-extras.gradle", "./platforms/android/app/build-extras.gradle");