The issue might have to do with how the route was built in the first place if there are multiple layers, the layers maybe linked. There's a term for that which I can't remember due to posting this away from my Trainz computer where I can take a look. If the layers are linked, then let's say something that is on the session layer, maybe linked back to the route layer so if, for example, you place a train car or consist this will force a route update as well.
What I have done, not for this reason since I didn't come across it, is to clone the route and clone the session(s). This produces new KUIDs of course. I then edit the config.txt file of the newly created session(s) and replace the route KUID with the one for my route. I have to remember, however, to also update that information in the KUID table as well.
Once that's done, I have my own copies of everything to mess around with and still have the original tucked away. If I plan on merging this route into one of my own, which I did with Midwest Grain 4.0 for example, and American Intermodal, I now have my own routes to mess around with to make the changes necessary for the merger.