In the a relationship of my model, go into the Edit mode and select the "Identifying" option and it adds new columns to the table entities, but when removing the option, the extra columns will not go away. This option affects many entities.
Upgrade to Toad Data Modeler 4.3 and the option to uncheck the "Identifying" will remove the new column generated in the table entities automatically in the Edit mode window.
The latest version of Toad Data Modeler can be downloaded here.