Last time I tried on a big application model was in 2007 and even after trying to get CA support to help, all concerned gave up after about a month on and off trying.
BUT I did not have StellaTools back then and deep knowledge about how triples and surrogates hold everything together under the covers in the plex model.
i Am ready to give this another go if you are. We need to export the smaller model, parse it, update it, import into the larger model. Try again, and try agin.
I remember it was the surrogates that in the end hurt us but this time we could use model api to replace. Let's talk off line and publish our findings latter if you want.