consider the project structure like following:
parent modules_group1 module1 module2 ....... modules_group2 moduleN moduleM ........
parent has modules module_group1, module_group2,....
each of these modules have submodules.
Open the parent as idea project: some submodules appear as nested not-module projects of parent, not as modules of their parents. The result of import may differ from time to time, and is different in different idea builds.
see attached project sample

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