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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