Not sure what to tell you here. The other user clearly deleted the files and the deletion was committed. It just wasn't activated. The modeler artifacts work a bit differently than other development objects. They will go looking of inactive states in other workspaces. For other development artifacts you could just delete that user's workspace and be OK.
The problem now is that the objects are pretty much already deleted and just pending the activation to process the deletion. How risky do you want to get here in trying to fix them? Can you afford to take a back up of the system and possibly restore if you mess up the clean up? If so you might try going into the _SYS_REPO schema and with SQL deleting the inactive state for this users workspace (from table INACTIVE_OBJECTS). This of course isn't supported by SAP, but if sucessful could remove the pending deletion status on these items and put them back to the way they were before that other user checked them out and deleted them.
