[{skill_id:2,skill_recs:[{_id:4,member_ids:[1,4,5]}]},{skill_id:5,skill_recs:[{_id:4,member_ids:[1,7,9]}]}]

db.collection.aggregate([{$unwind:"$skill_recs"},{$group:{_id:"$skill_recs._id",all_member_ids:{$push:"$skill_recs.member_ids"}}},{$addFields:{member_ids:{$reduce:{input:"$all_member_ids",initialValue:[],in:{$setUnion:["$$this","$$value"]}}}}}])