Jacob,
Sounds like you're having a real problem there. We just did some quick testing and couldn't get similar problem, not sure what's going on in your model. We could get that error message, but only when we actually modified the Duct System Family Type in one local, and tried to modify it again in the other local.
Try this to help troubleshoot:
!. Both users STC and Relinquish All.
2. Check your Worksets dialog, look at the Duct Types Element (see attached). Make sure that nobody is borrowing it.
3. Add a duct to the model, making a turn to add an Elbow.
4. Check the Worksets dialog again, see if you just took ownership of the Duct Types element.
If so, please log this issue with our support team and provide all the project files. We can't reproduce that behavior, so we would need your model to see what's causing it.
Kyle B
Kyle Bernhardt
Director
Building Design Strategy
Autodesk, Inc.