Yes, that’s what an auxiliary file is. It is a file that was passed as an argument to the deadlinecommand when performing the submission, which has the effect of copying the file to the Job folder in the Repository, and referencing it in the job’s metadata in the Database so plugins can access that file. When the Worker gets the Job, it copies over the Job folder from the Repository to the Deadline Temp. folder. This mechanism was designed mostly for scripts and text files needed by the submission, the option to send the scene file is a special case.
Now I wonder if you have relative paths in your scene, and when the scene gets copied around as auxiliary file it ends up cooking new .bgeo files when being loaded from the temp. folder, which ends up creating new .bgeo files there? Just a shot in the dark… Also, have you updated your hrender_dl.py script to the one we posted last week?