[{"key":"1,2,3,4,5,6"}]

db.collection.update({},[{$project:{key:{$filter:{input:{$split:["$key",","]},cond:{$ne:["$$this","3"]}}}}},{$project:{key:{$reduce:{input:"$key",initialValue:"",in:{$concat:["$$value",{"$cond":[{"$eq":["$$value",""]},"",", "]},"$$this"]}}}}}])