How to fix the settings of the gradle project so that after the dependency update an extra module does not appear?

After executing the “File > Invalidste Caches / Restart” command, the “Libraries” window of the project structure does not have all the dependencies.

The structure of the project modules in the "Modules" window is shown correctly.

I start dependency updates with the button in the tool window of the Gradle tool.

After updating, in the “Libraries” window of the “Project Structure” dialog, everything is fine.

But in the "Modules" window an extra module appears.

This is how the tree of project modules looks:

This is the Gradle settings:

This is the file "settings.gradle" of project:

This is the root file "build.gradle" of project:

This is the file "build.gradle" of application:

This is the file "build.gradle" of module ":domain":

For some reason, the in-project dependency does not work:

This is the file "build.gradle" of module ":bora":

Where, what and how to fix the project settings so that its structure remains correct after executing the command to update the project dependencies?