Criteria#eager_load writes the preloaded documents into a field named after the association (for example device), and hydration keeps that field in the document's attributes. Any write of the whole document, such as upsert or reassigning an embedded collection, then saves that copy, overwriting any data already stored under that name. Because the getter for a referenced association reads a stored field with the association's name instead of querying, later loads keep returning the stale copy. A fix is proposed in https://github.com/mongodb/mongoid/pull/6202.

class Device
  include Mongoid::Document
end

class Port
  include Mongoid::Document
  belongs_to :device
end

device = Device.create!
port = Port.create!(device: device)

Port.eager_load(:device).first.upsert

Port.collection.find(_id: port.id).first
# => { "_id" => ..., "device_id" => ..., "device" => [ { "_id" => ... } ] }