I do not think that there are any changes made in that direction at all. Maybe the UpdateDatabase property of the project somehow has changed to True. In such cases it is required that the mapping configuration is present in the config file.
However to make sure that only the invalid references will be fixed and nothing else, you can disable the mapping validations of the Check Settings wizard and run only the upgrade functionality. To do that, for each project in the Targets treeview disable all validators from the Validators treeview and enable only the "Update assembly references" validator.
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