I received another option from Autodesk concerning the duct under a transition not hiding. I liked this idea and thought you all should know about it as well.
Draw a duct (doesn't matter what system you choose) that is an inch or two wider than the duct that is running underneath your transition, the smallest height possible (I think that is 3"), and only as long as the transition. Now select that duct and change its layer to your -Nplt layer. In elevation: you need to place this duct just underneath the transition, but above the duct that you want to show as hidden. You may have to go into an elevation view to make sure you get everything aligned. Once you have the elevation aligned you need to align it to be directly over the duct run you want to show hidden. You must make sure that your -Nplt layer is truly a non-plotting layer (verify in the layer manager that the print symbol has a red slash through it for this layer). Now go into paperspace and do a print preview and verify that you have hidden what you needed to, and nothing more. I have tested this out and it seems to work.
Here is an ortho view and a plan view of the results:
Post-script here....in some cases we have very tight clearances and the 3" duct height won't work. You can use a 1/4" diameter pipe and it will force the duct to hide under that as well. You might have to do one pipe over each side of the duct. Just a thought.