In an individual flavor's sourceSet, you don't need to specify the main sourceSet. You can put common code in src/main and it will be picked up without needing to explicitly reference it from other flavors.
I'm not sure how it worked before.
If you remove that, you don't in fact need your sourceSets
block at all -- the default behavior is to put common code in src/main and flavor-specific code in src/flavor-name, like how you already have it set up.