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Question
Can a Cohen visit ancient archeological sites that have burial caves that do nit contain full skeletons?
Answer
ב"ה
Shalom
In the Hebrew counterpart of this website, Rav Ya'akov Ariel Shlit"a answered this question when asked in regard to a Cohen visiting Bet She'arim, which a burial site from the time of the Tanaim.
Rav Ya'akov Ariel ruled that even if we're to assume that all the bones were removed, which is not totally clear, the "golel and dofek", which are parts of tombs ( there are different interpretations among the commentators, but basically the tomb and its cover) still can make Cohanim Tamei, therefore a Cohen may not visit in these places.
(See Shulchan Aruch Yoreh De'ah 369:1, where it says that a Cohen is warned not to become Tamei to the "golel and dofek".)
All the best

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