I put a post in the general discussion section about whether a factory file needed to have an updated STL file loaded every time a revision was made to the STL. The answers suggested that you do need to remove and re-insert each new version of an STL file. This seems like a lot of un-necessary work especially for a user-designed file that may be very similar from one version to the next.
I would think it better if the factory file is linked to a STL file and as long as the filename and location are preserved the software would update on load to the latest saved configuration (in the location) and re-create the slicing process according to the process and other settings in the factory file. This would be much more efficient to not have to re-create part locations, different settings, supports, rafts etc from scratch. If you wanted to preserve an original factory file with the prior version you would not over-write the updated version and give it a different name (original_2 for example).