I was recently informed that light fixtures in my MEP file were not visible in the architect's reflected ceiling plan. Upon performing an experiment, I determined that Revit does not necessarily link a file at the same elevation. In my experiment, I created an architectural model with walls, floor, and lay-in ceiling. I then created an MEP file, linked the architectural file, and placed light fixtures, diffusers, ductwork, and air handling units. Then, I returned to Revit Architecture, opened the architectural model, and linked the MEP file to it. I displayed the RCP and found -- NO light fixtures. (This was in the Hidden Line visual style--they were visible in wireframe.) I cut a section, and found that the MEP file levels were off by 9-1/4". I lowered the MEP file so that the levels coincided, and the light fixtures and diffusers appeared in the RCP with the Hidden Line visual style displayed.
I suspect that allowing Revit to make the line using Center to Center causes the problem. I repeated the experiment using Origin to Origin, and the MEP model was linked at the correct elevation.
From the several options to link a model, only Origin to Origin and Shared Coordinates are reliable. Center to Center is not, because the center changes every time the bounding box that includes all the elements changes size when you add or remove objects. That option should not be used for linking models, except as a temporary means of bringing something in, without precision.