class Jam
  include Mongoid::Document
  embedded_in :womp
end

class Womp
  include Mongoid::Document
  embeds_many :jams
  accepts_nested_attributes_for :jams, allow_destroy: true
end

w = Womp.create!

w.attributes
#=> {"_id"=>BSON::ObjectId('58489d22a54d75c13c000006')}

w.update_attributes({ jams_attributes: [ {} ] })

w.attributes
#=> {"_id"=>BSON::ObjectId('58489d22a54d75c13c000006')}

w.reload.attributes
#=> {"_id"=>BSON::ObjectId('58489d22a54d75c13c000006'), "jams"=>[{"_id"=>BSON::ObjectId('58489d22a54d75c13c000007')}]}

w.update_attributes({ jams_attributes: [ { id: w.jams.first.id, _destroy: true } ] })

w.attributes
#=> {"_id"=>BSON::ObjectId('58489d22a54d75c13c000006'), "jams"=>[{"_id"=>BSON::ObjectId('58489d22a54d75c13c000007')}]}

w.reload.attributes
#=> {"_id"=>BSON::ObjectId('58489d63a54d75c13c000008'), "jams"=>[]}