When you create then apply (with the API) view filters on view plans that have "linked" parts, these view filters can also be applied on the linked parts.
However :
- it has to be rule-based filters. Selection-based filters don't work : you can add to a newly created view filter (which resides in the main document) IDs of elements that belong to a linked document, but that will do nothing because Revit looks for elements in the main document (you can end up filtering elements in the main document that you don't want, if IDs are similar !).
With the UI : you cannot add an element from a linked model to a selection set for filter
- rule-based filters that use parameters stored with an ElementId (like levels, etc) don't work because these IDs values refer to elements from the main document...
With the UI : you can make for instance a rule-based filter for rooms based on level parameter (BuiltInParameter.ROOM_LEVEL_ID). But the possible values are levels from the main document only, you don't have the levels whose IDs reside in linkeds documents.