Jury rig config should be kept until the component in question has a repair done on it at Enceladus.
The use case is when you have a component that's not worth it to repair since it okay for the time being, and you tuned it so that the damage affects a stat that's less important to you. Currently, at the beginning of a dive, these changes have to be re-applied every time.
In case people forget to reset it, the auto-reset should still happen when the part is fixed.
In universe, this would be the duct taped/hotwired solution being removed once the parts are available to fix it properly. However, if you don't have time for maintenance and immediately go back to the rings, the modification would stay.