Yes, your assuption is correct. You need to consolidate.
In addition to the normal "on-board means", you can do the consolidation manually.
I would recommend doing that automatically. After importing data, you could use a report script (which you'd need to write), which searches for a predefined set of models for objects having the same name and does the consolidation.
We are currently undergoing a similar mass import of ARIS Express models into our ARIS repository and are looking to speed up the consolidation process. I am still very inexperienced with script writing. Has anyone written a script for this they would be willing to share? Or pointers on creating it would work too.