I did an experiment and found that the custom user-defined property I made was retained through a model update, although I didn't do an exhaustive test of all possible options.
In my federated NWF model, I made a custom property on a DWG file that is in a "container" NWD model. I went into AutoCAD and made an edit to that DWG, then I updated the NWF of the container model (where I noted that the properties of the DWG in the container model did not include my custom one), saved it as an NWD, and finally opened my federated NWF. The custom property I made was still shown in the DWG's properties here, so this leads me to understand that the custom property "lives" in the Navisworks model it was created in, and as long as the model that the property was added to is present, the custom property will continue to be included on that specific object/file/model.