Removing a Project Module / Importing a Module

Certain actions on module groups appear to remove all my projects module groups without a logical reason for doing so.

Example

I have imported a bunch of existing maven projects as modules into my project.

I've organised these modules under module groups for those maven projects that are logically related.

If i do any of the following all module groups are removed from the project.

1. Import a module from a multi-module maven project and use the option create module groups for multi-module maven projects when importing.
2. If i delete any module group, all other unrelated module groups are removed.

This is becoming incredibly frustrating as it's a tedious process to re-create these groups every-time i find an action that trashes my Project. I have over a hundred modules at the moment and it's hard to navigate effectively without being able to define some sort of hierarchy.