While creating a single package iModel (i.dgn) of a DGN file with multiple reference file, there is an option to select "Remove Intermediate Files".

However, when a user is working on a ProjectWise integrated session of Microstation, and create a Single Package iModel with "Remove Intermediate Files" checked on, PW still uploads all the Reference i.DGN file that are created, which will eventually be deleted.

If a DGN file has 100 references, then each i.dgn file is uploaded to PW and then deleted once the Single Package iModel is created. This process can be improved by preventing the upload of intermediate files to PW if the "Remove Intermediate Files" box is checked.