[{"_id":{"$oid":"6241dd90891458501c17d627"},"A":[{"_id":{"$oid":"6241ddb1891458501c17d63e"},"B":[{"_id":{"$oid":"6241ddc4891458501c17d674"}},{"_id":{"$oid":"6241ddda891458501c17d675"}}]},{"_id":{"$oid":"6241ddbe891458501c17d63f"},"B":[{"_id":{"$oid":"6241ddda891458501c17d678"}},{"_id":{"$oid":"6241ddda891458501c17d679"}}]}]}]

db.collection.aggregate([{$match:{"A.B._id":{"$oid":"6241ddda891458501c17d679"}}},{"$addFields":{"A":{"$filter":{"input":{"$map":{"input":"$A","as":"a","in":{"_id":"$$a._id","B":{"$filter":{"input":"$$a.B","as":"b","cond":{"$eq":[{"$oid":"6241ddda891458501c17d679"},"$$b._id"]}}}}}},"as":"an","cond":{"$ne":["$$an.B",[]]}}}}}])