That's pretty similar to what I'm trying to do. In my case I already had the project imported and I split it into a multiproject build. Do I need to reimport the project into intellij?
The easiest way is to re-import the whole project.
Alternatively you can refresh project structure, import all gradle-local project structure entities and remove all ide-local entities.
Please note that gradle auto-import is on the way (will be imlemented this or the next week). It will be possible to manually update the plugin to use the feature. So, feel free to keep track on gradle improvements.