Another observation, if the generated class is too big, then IDEA disables the code insight. Apparently this has side effect which also makes the class out of source code (I can see the icon change of the generated class). For IDEA, just adding property "idea.max.intellisense.filesize=5242880" which is greater than the generated file size solved my problem. I think this is a bug.

Above is added as comment to https://youtrack.jetbrains.com/issue/IDEA-209418/Gradle-generated-Protobuf-Java-sources-are-not-detected-added-as-module-dependencies-for-Gradle-project-korlin-dsl#focus=Comments-27-12449342.0-0

Hope helps to someone ...