I'm also (absolutely) sure the answer is: it can't be done, anyway, at least with different routes.

A scenario is made using track markers of a certain route... one single missing track marker is enough to break the scenario, wonder all of them missed!
However, in your case (a cloned route with same track markers) it may work. And this is very simple and fast to you test: clone a route, change some few scenery itens, clone the scenario from original route, copy and paste it into the \ClonedRoute0000-000000\Scenarios folder and see what happens.
Cheers,
Doc.
Edited later: in the other trainsim game you can edit the route whenever and whatever you want for each "scenario" (aka "mission" or "activity"). The changes on the route are applied only for that mission, original route is not changed. And, yes, I'm talking about changings in the track layout, i.e., add/modify/remove tracks, junctions, turntables etc. Maybe, and hopefully, some day in a distant future here on RW also....
Who doesn't have dog, hunts with cat.