Outline from a conversation with dagmar via IRC:

Currently 2.x version of exportable doesn't take care of the exportables table when a feature is disabled so the data is kept until it is reused when the feature is enabled or it gets deleted when exportables module is uninstalled.

So, when a feature is disabled, there is no way of keeping trace if the data of exportables is longer valid or not.

I think that when a feature is disabled, the exportables data associated should be deleted because if it is enabled again, as soon as the modules or features page is visited, the elements get populated again in the exportables table.

Ideally, when the feature is disabled and one element with the same machine name is created manually or imported, if the feature is enabled again, it should appear with "overriden" status.