Yes, there is a way. The Controller Panel settings are lost when switching between projects because the detectors selected in the Queue Settings of Queue Setup are not the same in both projects. Before attaching the CCU to a new project, check to make sure that the detectors selected are the same in both projects:
Here we have a CC13 for both the field and reference. As long as both projects have the same detectors selected, the CCU setup will carry over to the other project.