When scheduling items, such as Doors, and you include linked elements, Revit will not allow the schedule to be filtered by level any longer. I believe this is because Revit does not know what level in a linked model corresponds to the level in the model that has the schedule. One simple solution is to 'link' the levels to other models based on their height, since they may have different names. Otherwise, a way to set up a linking scheme through a dialog, similar to how Phase Mapping is set for a linked model.
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