A constant issue I deal with is when changing ductwork from one phase to a later phase, the duct lining remains in the previous phase. When navigating the Revit interface these linings are not visible, but they do plot. Correcting this is tedious. I have to select each bit of duct, click on edit lining, and change the phase.
I can tell you that nobody ever goes into an existing building and installs liner in existing ductwork. It is more economical to replace the ductwork with a new piece of duct which was lined in the shop. There is no reason duct lining should be able to be in a different phase than the duct is.
Insulations are a different story, because they can be installed around the outside of the duct. But Revit ought to automatically adjust the phase of duct linings to match the duct phase.