I am using DeepSave to successfully save an object with multiple relations, but I have noticed that the ownerId object is no longer saved in the database, which was not the case previously. The object is saved with an authenticated user.
Just checked Codeless and REST deep save logic and was unable to reproduce your problem. Could you please post here screen of logic where you perform user login and deep save call? It seems to me that there is no user token available when deep save is called.