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The message you get is triggered when you remove/delete a model and do a migration.
In most cases, you can delete them safely. However, in some cases this might result to data loss. If other models have a foreign key to the removed model, these objects will also be deleted.
Here’s the django ticket that requests to make deleting stale content types safer.
EDIT
As @x-yuri pointed, this ticket has been fixed and has been released in Django 1.11.
Source:stackexchange.com