[kovidgoyal]

If find duplicates wishes to store a set of books between sessions, it needs to do it in some fashion other than using marks. Or, more precisely, it is already storing excluded books using some mechanism other than marks (since marks are strictly temporary). It is then applying marks to all those stored books, presumably on calibre startup. It should not do that, instead it should mark books only when it is run. Since originally, marks were not displayed in the UI unless the user ran the marked:true search, find duplicates' behavior was acceptable, it isn't any more. There is nothing that core calibre can do to prevent a plugin like find duplicates from abusing marked books in this way.